Abstract
Chromosomes are constantly damaged by exogenous and endogenous factors. To cope with DNA damage, eukaryotic cells are equipped with three phosphatidylinositol 3-kinase-related kinases (PIKKs), such as ATM, ATR, and DNA-PK. PIKKs are structurally related to phosphatidylinositol 3-kinase (lipid kinase), however possess protein kinase activities. The Mre11–Rad50–Nbs1 and the Ku complex interact with and activate ATM and DNA-PKcs at double-stranded DNA breaks (DSBs), respectively. In contrast, ATR responds to various types of DNA lesions by interacting with replication protein A (RPA)-covered single-stranded DNA (ssDNA). Several lines of evidence have established a model in which ATR is activated by interacting with ATR activating proteins including TopBP1 and ETAA1 at DNA lesions in humans, yet the interaction of ATR with RPA-covered ssDNA does not result in ATR activation. In budding yeast, the Mec1–Ddc2 complex (Mec1–Ddc2) corresponds to ATR–ATRIP. Similar to ATR, Mec1 activation is accomplished by interactions with Mec1 activating proteins, which are Ddc1, Dpb11 (TopBP1 homolog) and Dna2. However, recent studies provide results supporting the idea that Mec1ATR is also activated by interacting with RPA-covered ssDNA tracts. These observations suggest that all the ATM, ATR, DNA-PK family proteins can be activated immediately upon DNA damage recognition.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Ball HL, Ehrhardt MR, Mordes DA, Glick GG, Chazin WJ, Cortez D (2007) Function of a conserved checkpoint recruitment domain in ATRIP proteins. Mol Cell Biol 27(9):3367–3377. https://doi.org/10.1128/MCB.02238-06
Bandhu A, Kang J, Fukunaga K, Goto G, Sugimoto K (2014) Ddc2 mediates Mec1 activation through a Ddc1- or Dpb11-independent mechanism. PLoS Genet 10(2):e1004136. https://doi.org/10.1371/journal.pgen.1004136
Bando M, Katou Y, Komata M, Tanaka H, Itoh T, Sutani T et al (2009) Csm3, Tof1, and Mrc1 form a heterotrimeric mediator complex that associates with DNA replication forks. J Biol Chem 284(49):34355–34365. https://doi.org/10.1074/jbc.m109.065730
Bass TE, Luzwick JW, Kavanaugh G, Carroll C, Dungrawala H, Glick GG et al (2016) ETAA1 acts at stalled replication forks to maintain genome integrity. Nat Cell Biol 18(11):1185–1195. https://doi.org/10.1038/ncb3415
Biswas H, Goto G, Wang W, Sung P, Sugimoto K (2019) Ddc2ATRIP promotes Mec1ATR activation at RPA–ssDNA tracts. PLoS Genet 15(8):e1008294. https://doi.org/10.1371/journal.pgen.1008294
Blackford AN, Jackson SP (2017) ATM, ATR, and DNA-PK: the trinity at the heart of the DNA damage response. Mol Cell 66(6):801–817. https://doi.org/10.1016/j.molcel.2017.05.015
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(1):87–96. https://doi.org/10.1007/s00294-017-0727-2
Cannavo E, Cejka P, Kowalczykowski SC (2013) Relationship of DNA degradation by Saccharomyces cerevisiae exonuclease 1 and its stimulation by RPA and Mre11-Rad50-Xrs2 to DNA end resection. Proc Natl Acad Sci USA 110(18):E1661–E1668. https://doi.org/10.1073/pnas.1305166110
Cejka P, Cannavo E, Polaczek P, Masuda-Sasa T, Pokharel S, Campbell JL et al (2010) DNA end resection by Dna2-Sgs1-RPA and its stimulation by Top3-Rmi1 and Mre11-Rad50-Xrs2. Nature 467(7311):112–116. https://doi.org/10.1038/nature09355
Chen R, Wold MS (2014) Replication protein A: single-stranded DNA’s first responder: dynamic DNA-interactions allow replication protein A to direct single-strand DNA intermediates into different pathways for synthesis or repair. Bioessays 36(12):1156–1161. https://doi.org/10.1002/bies.201400107
Chen SH, Zhou H (2009) Reconstitution of Rad53 activation by Mec1 through adaptor protein Mrc1. J Biol Chem 284(28):18593–18604. https://doi.org/10.1074/jbc.m109.018242
Chen X, Niu H, Chung WH, Zhu Z, Papusha A, Shim EY et al (2011) Cell cycle regulation of DNA double-strand break end resection by Cdk1-dependent Dna2 phosphorylation. Nat Struct Mol Biol 18(9):1015–1019. https://doi.org/10.1038/nsmb.2105
Chen H, Lisby M, Symington LS (2013) RPA coordinates DNA end resection and prevents formation of DNA hairpins. Mol Cell 50(4):589–600. https://doi.org/10.1016/j.molcel.2013.04.032
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(3):657–661. https://doi.org/10.1007/s00294-018-0920-y
Coutelier H, Xu Z (2019) Adaptation in replicative senescence: a risky business. Curr Genet 65(3):711–716. https://doi.org/10.1007/s00294-019-00933-7
Cussiol JR, Jablonowski CM, Yimit A, Brown GW, Smolka MB (2015) Dampening DNA damage checkpoint signalling via coordinated BRCT domain interactions. EMBO J 34(12):1704–1717. https://doi.org/10.15252/embj.201490834
Deshpande I, Seeber A, Shimada K, Keusch JJ, Gut H, Gasser SM (2017) Structural basis of Mec1–Ddc2–RPA assembly and activation on single-stranded DNA at sites of damage. Mol Cell 68(2):431–445. https://doi.org/10.1016/j.molcel.2017.09.019
Elledge SJ (1996) Cell cycle checkpoints: preventing an identity crisis. Science 274:1664–1672
Ferretti LP, Lafranchi L, Sartori AA (2013) Controlling DNA-end resection: a new task for CDKs. Front Genet 4:99. https://doi.org/10.3389/fgene.2013.00099
Furuya K, Poitelea M, Guo L, Caspari T, Carr AM (2004) Chk1 activation requires Rad9 S/TQ-site phosphorylation to promote association with C-terminal BRCT domains of Rad4TOPBP1. Genes Dev 18(10):1154–1164. https://doi.org/10.1101/gad.291104
Germann SM, Oestergaard VH, Haas C, Salis P, Motegi A, Lisby M (2011) Dpb11/TopBP1 plays distinct roles in DNA replication, checkpoint response and homologous recombination. DNA Repair (Amst) 10(2):210–224. https://doi.org/10.1016/j.dnarep.2010.11.001
Granata M, Lazzaro F, Novarina D, Panigada D, Puddu F, Abreu CM et al (2010) Dynamics of Rad9 chromatin binding and checkpoint function are mediated by its dimerization and are cell cycle-regulated by CDK1 activity. PLoS Genet. https://doi.org/10.1371/journal.pgen.1001047
Haahr P, Hoffmann S, Tollenaere MA, Ho T, Toledo LI, Mann M et al (2016) Activation of the ATR kinase by the RPA-binding protein ETAA1. Nat Cell Biol 18(11):1196–1207. https://doi.org/10.1038/ncb3422
Harari Y, Kupiec M (2018) Mec1(ATR) is needed for extensive telomere elongation in response to ethanol in yeast. Curr Genet 64(1):223–234. https://doi.org/10.1007/s00294-017-0728-1
Harper JW, Elledge SJ (2007) The DNA damage response: 10 years after. Mol Cell 28(5):739–745
Kumar S, Burgers PM (2013) Lagging strand maturation factor Dna2 is a component of the replication checkpoint initiation machinery. Genes Dev 27(3):313–321. https://doi.org/10.1101/gad.204750.112
Lanz MC, Oberly S, Sanford EJ, Sharma S, Chabes A, Smolka MB (2018) Separable roles for Mec1/ATR in genome maintenance, DNA replication, and checkpoint signaling. Genes Dev 32(11–12):822–835. https://doi.org/10.1101/gad.308148.117
Lee YC, Zhou Q, Chen J, Yuan J (2016) RPA-binding protein ETAA1 is an ATR activator involved in DNA replication stress response. Curr Biol 26(24):3257–3268. https://doi.org/10.1016/j.cub.2016.10.030
Lin SJ, Wardlaw CP, Morishita T, Miyabe I, Chahwan C, Caspari T et al (2012) The Rad4(TopBP1) ATR-activation domain functions in G1/S phase in a chromatin-dependent manner. PLoS Genet 8(6):e1002801. https://doi.org/10.1371/journal.pgen.1002801
Lou H, Komata M, Katou Y, Guan Z, Reis CC, Budd M et al (2008) Mrc1 and DNA polymerase epsilon function together in linking DNA replication and the S phase checkpoint. Mol Cell 32(1):106–117. https://doi.org/10.1016/j.molcel.2008.08.020
Majka J, Niedziela-Majka A, Burgers PM (2006) The checkpoint clamp activates Mec1 kinase during initiation of the DNA damage checkpoint. Mol Cell 24(6):891–901. https://doi.org/10.1016/j.molcel.2006.11.027
Mordes DA, Nam EA, Cortez D (2008a) Dpb11 activates the Mec1–Ddc2 complex. Proc Natl Acad Sci USA 105(48):18730–18734. https://doi.org/10.1073/pnas.0806621105
Mordes DA, Glick GG, Zhao R, Cortez D (2008b) TopBP1 activates ATR through ATRIP and a PIKK regulatory domain. Genes Dev 22(11):1478–1489
Navadgi-Patil VM, Burgers PM (2008) Yeast DNA replication protein Dpb11 activates the Mec1/ATR checkpoint kinase. J Biol Chem 283(51):35853–35859
Navadgi-Patil VM, Burgers PM (2009) The unstructured C-terminal tail of the 9-1-1 clamp subunit Ddc1 activates Mec1/ATR via two distinct mechanisms. Mol Cell 36(5):743–753. https://doi.org/10.1016/j.molcel.2009.10.014
Navadgi-Patil VM, Kumar S, Burgers PM (2011) The unstructured C-terminal tail of yeast Dpb11 (human TopBP1) protein is dispensable for DNA replication and the S phase checkpoint but required for the G2/M checkpoint. J Biol Chem 286(47):40999–41007. https://doi.org/10.1074/jbc.M111.283994
Niu H, Chung WH, Zhu Z, Kwon Y, Zhao W, Chi P et al (2010) Mechanism of the ATP-dependent DNA end-resection machinery from Saccharomyces cerevisiae. Nature 467(7311):108–111
Ogiwara H, Ui A, Onoda F, Tada S, Enomoto T, Seki M (2006) Dpb11, the budding yeast homolog of TopBP1, functions with the checkpoint clamp in recombination repair. Nucleic Acids Res 34(11):3389–3398. https://doi.org/10.1093/nar/gkl411
Ohouo PY, Bastos de Oliveira FM, Almeida BS, Smolka MB (2010) DNA damage signaling recruits the Rtt107-Slx4 scaffolds via Dpb11 to mediate replication stress response. Mol Cell 39(2):300–306. https://doi.org/10.1016/j.molcel.2010.06.019
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
Paciotti V, Lucchini G, Plevani P, Longhese MP (1998) Mec1p is essential for phosphorylation of the yeast DNA damage checkpoint protein Ddc1p, which physically interacts with Mec3p. EMBO J 17:4199–4209
Paull TT (2015) Mechanisms of ATM activation. Annu Rev Biochem. https://doi.org/10.1146/annurev-biochem-060614-034335
Pfander B, Diffley JF (2011) Dpb11 coordinates Mec1 kinase activation with cell cycle-regulated Rad9 recruitment. EMBO J 30(24):4897–4907. https://doi.org/10.1038/emboj.2011.345
Pokhrel N, Caldwell CC, Corless EI, Tillison EA, Tibbs J, Jocic N et al (2019) Dynamics and selective remodeling of the DNA-binding domains of RPA. Nat Struct Mol Biol 26(2):129–136. https://doi.org/10.1038/s41594-018-0181-y
Puddu F, Granata M, Di Nola L, Balestrini A, Piergiovanni G, Lazzaro F et al (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(15):4782–4793
Rouse J, Jackson SP (2002) Lcd1p recruits Mec1p to DNA lesions in vitro and in vivo. Mol Cell 9:857–869
Saldivar JC, Cortez D, Cimprich KA (2017) The essential kinase ATR: ensuring faithful duplication of a challenging genome. Nat Rev Mol Cell Biol 18(10):622–636. https://doi.org/10.1038/nrm.2017.67
Schwartz MF, Duong JK, Sun Z, Morrow JS, Pradhan D, Stern DF (2002) Rad9 phosphorylation sites couple Rad53 to the Saccharomyces cerevisiae DNA damage checkpoint. Mol Cell 9:1055–1065
Singh B, Wu PJ (2019) Linking the organization of DNA replication with genome maintenance. Curr Genet 65(3):677–683. https://doi.org/10.1007/s00294-018-0923-8
Smith GC, Jackson SP (1999) The DNA-dependent protein kinase. Genes Dev 13(8):916–934
Sugimoto K (2018) Branching the Tel2 pathway for exact fit on phosphatidylinositol 3-kinase-related kinases. Curr Genet 64(5):965–970. https://doi.org/10.1007/s00294-018-0817-9
Sweeney FD, Yang F, Chi A, Shabanowitz J, Hunt DF, Durocher D (2005) Saccharomyces cerevisiae Rad9 acts as a Mec1 adaptor to allow Rad53 activation. Curr Biol 15(15):1364–1375
Taylor MRG, Yeeles JTP (2018) The initial response of a eukaryotic replisome to DNA damage. Mol Cell 70(6):1067–1080. https://doi.org/10.1016/j.molcel.2018.04.022
Vialard JE, Gilbert CS, Green CM, Lowndes NF (1998) The budding yeast Rad9 checkpoint protein is subjected to Mec1/Tel1-dependent hyperphosphorylation and interacts with Rad53 after DNA damage. EMBO J 17:5679–5688
Wang X, Ran T, Zhang X, Xin J, Zhang Z, Wu T et al (2017) 3.9 A structure of the yeast Mec1–Ddc2 complex, a homolog of human ATR-ATRIP. Science 358(6367):1206–1209. https://doi.org/10.1126/science.aan8414
Wardlaw CP, Carr AM, Oliver AW (2014) TopBP1: a BRCT-scaffold protein functioning in multiple cellular pathways. DNA Repair (Amst) 22:165–174. https://doi.org/10.1016/j.dnarep.2014.06.004
Wold MS (1997) Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu Rev Biochem 66:61–92
Yates LA, Aramayo RJ, Pokhrel N, Caldwell CC, Kaplan JA, Perera RL et al (2018) A structural and dynamic model for the assembly of replication protein A on single-stranded DNA. Nature Commun 9(1):5447. https://doi.org/10.1038/s41467-018-07883-7
Yazinski SA, Zou L (2016) Functions, regulation, and therapeutic implications of the ATR checkpoint pathway. Annu Rev Genet 50:155–173. https://doi.org/10.1146/annurev-genet-121415-121658
Yue M, Zeng L, Singh A, Xu Y (2014) Rad4 mainly functions in Chk1-mediated DNA damage checkpoint pathway as a scaffold protein in the fission yeast Schizosaccharomyces pombe. PLoS One 9(3):e92936. https://doi.org/10.1371/journal.pone.0092936
Zhou B-BS, Elledge SJ (2000) The DNA damage response: putting checkpoints in perspective. Nature 408:433–439
Zhou C, Pourmal S, Pavletich NP (2015) Dna2 nuclease-helicase structure, mechanism and regulation by Rpa. Elife. https://doi.org/10.7554/elife.09832
Zou L, Elledge SJ (2003) Sensing DNA damage through ATRIP recognition of RPA–ssDNA complexes. Science 300:1542–1548
Acknowledgements
This work was supported by Grant GM120730 (KS) from National Institute of Health (http://www.nih.gov).
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by M. Kupiec.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Ma, M., Rodriguez, A. & Sugimoto, K. Activation of ATR-related protein kinase upon DNA damage recognition. Curr Genet 66, 327–333 (2020). https://doi.org/10.1007/s00294-019-01039-w
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00294-019-01039-w