Role of PCNA and RFC in promoting Mus81-complex activity

. 2017 Oct 02 ; 15 (1) : 90. [epub] 20171002

Jazyk angličtina Země Anglie, Velká Británie Médium electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid28969641
Odkazy

PubMed 28969641
PubMed Central PMC5625722
DOI 10.1186/s12915-017-0429-8
PII: 10.1186/s12915-017-0429-8
Knihovny.cz E-zdroje

BACKGROUND: Proper DNA replication is essential for faithful transmission of the genome. However, replication stress has serious impact on the integrity of the cell, leading to stalling or collapse of replication forks, and has been determined as a driving force of carcinogenesis. Mus81-Mms4 complex is a structure-specific endonuclease previously shown to be involved in processing of aberrant replication intermediates and promotes POLD3-dependent DNA synthesis via break-induced replication. However, how replication components might be involved in this process is not known. RESULTS: Herein, we show the interaction and robust stimulation of Mus81-Mms4 nuclease activity by heteropentameric replication factor C (RFC) complex, the processivity factor of replicative DNA polymerases that is responsible for loading of proliferating cell nuclear antigen (PCNA) during DNA replication and repair. This stimulation is enhanced by RFC-dependent ATP hydrolysis and by PCNA loading on the DNA. Moreover, this stimulation is not specific to Rfc1, the largest of subunit of this complex, thus indicating that alternative clamp loaders may also play a role in the stimulation. We also observed a targeting of Mus81 by RFC to the nick-containing DNA substrate and we provide further evidence that indicates cooperation between Mus81 and the RFC complex in the repair of DNA lesions generated by various DNA-damaging agents. CONCLUSIONS: Identification of new interacting partners and modulators of Mus81-Mms4 nuclease, RFC, and PCNA imply the cooperation of these factors in resolution of stalled replication forks and branched DNA structures emanating from the restarted replication forks under conditions of replication stress.

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Heller R, Marians K. Replisome assembly and the direct restart of stalled replication forks. Nat Rev Mol Cell Biol. 2006;7(12):932–43. doi: 10.1038/nrm2058. PubMed DOI

Mazouzi A, Velimezi G, Loizou JI. DNA replication stress: causes, resolution and disease. Exp Cell Res. 2014;329(1):85–93. doi: 10.1016/j.yexcr.2014.09.030. PubMed DOI

Raveendranathan M, Chattopadhyay S, Bolon YT, Haworth J, Clarke DJ, Bielinsky AK. Genome-wide replication profiles of S-phase checkpoint mutants reveal fragile sites in yeast. EMBO J. 2006;25(15):3627–39. doi: 10.1038/sj.emboj.7601251. PubMed DOI PMC

Nyberg KA, Michelson RJ, Putnam CW, Weinert TA. Toward maintaining the genome: DNA damage and replication checkpoints. Annu Rev Genet. 2002;36:617–56. doi: 10.1146/annurev.genet.36.060402.113540. PubMed DOI

Jackson SP, Bartek J. The DNA-damage response in human biology and disease. Nature. 2009;461(7267):1071–8. doi: 10.1038/nature08467. PubMed DOI PMC

Osman F, Whitby M. Exploring the roles of Mus81-Eme1/Mms4 at perturbed replication forks. DNA Repair. 2007;6(7):1004–17. doi: 10.1016/j.dnarep.2007.02.019. PubMed DOI

Ira G, Malkova A, Liberi G, Foiani M, Haber JE. Srs2 and Sgs1-Top3 suppress crossovers during double-strand break repair in yeast. Cell. 2003;115(4):401–11. doi: 10.1016/S0092-8674(03)00886-9. PubMed DOI PMC

Muñoz-Galván S, Tous C, Blanco MG, Schwartz EK, Ehmsen KT, West SC, Heyer WD, Aguilera A. Distinct roles of Mus81, Yen1, Slx1-Slx4, and Rad1 nucleases in the repair of replication-born double-strand breaks by sister chromatid exchange. Mol Cell Biol. 2012;32(9):1592–603. doi: 10.1128/MCB.00111-12. PubMed DOI PMC

Ciccia A, McDonald N, West SC. Structural and functional relationships of the XPF/MUS81 family of proteins. Annu Rev Biochem. 2008;77:259–87. doi: 10.1146/annurev.biochem.77.070306.102408. PubMed DOI

Szakal B, Branzei D. Premature Cdk1/Cdc5/Mus81 pathway activation induces aberrant replication and deleterious crossover. EMBO J. 2013;32(8):1155–67. doi: 10.1038/emboj.2013.67. PubMed DOI PMC

Gallo-Fernández M, Saugar I, Ortiz-Bazán M, Vázquez MV, Tercero JA. Cell cycle-dependent regulation of the nuclease activity of Mus81-Eme1/Mms4. Nucleic Acids Res. 2012;40(17):8325–35. doi: 10.1093/nar/gks599. PubMed DOI PMC

Matos J, West SC. Holliday junction resolution: regulation in space and time. DNA Repair (Amst) 2014;19:176–81. doi: 10.1016/j.dnarep.2014.03.013. PubMed DOI PMC

Princz LN, Wild P, Bittmann J, Aguado FJ, Blanco MG, Matos J, Pfander B. Dbf4-dependent kinase and the Rtt107 scaffold promote Mus81-Mms4 resolvase activation during mitosis. EMBO J. 2017;36(5):664–78. doi: 10.15252/embj.201694831. PubMed DOI PMC

Matos J, Blanco MG, Maslen S, Skehel JM, West SC. Regulatory control of the resolution of DNA recombination intermediates during meiosis and mitosis. Cell. 2011;147(1):158–72. doi: 10.1016/j.cell.2011.08.032. PubMed DOI PMC

Duda H, Arter M, Gloggnitzer J, Teloni F, Wild P, Blanco MG, Altmeyer M, Matos J. A mechanism for controlled breakage of under-replicated chromosomes during mitosis. Dev Cell. 2016;39(6):740–55. doi: 10.1016/j.devcel.2016.11.017. PubMed DOI

Sebesta M, Urulangodi M, Stefanovie B, Szakal B, Pacesa M, Lisby M, Branzei D, Krejci L. Esc2 promotes Mus81 complex-activity via its SUMO-like and DNA binding domains. Nucleic Acids Res. 2017;45(1):215–30. doi: 10.1093/nar/gkw882. PubMed DOI PMC

Zhang R, Sengupta S, Yang Q, Linke SP, Yanaihara N, Bradsher J, Blais V, McGowan CH, Harris CC. BLM helicase facilitates Mus81 endonuclease activity in human cells. Cancer Res. 2005;65(7):2526–31. doi: 10.1158/0008-5472.CAN-04-2421. PubMed DOI

Matulova P, Marini V, Burgess R, Sisakova A, Kwon Y, Rothstein R, Sung P, Krejci L. Cooperativity of Mus81.Mms4 with Rad54 in the resolution of recombination and replication intermediates. J Biol Chem. 2009;284(12):7733–45. doi: 10.1074/jbc.M806192200. PubMed DOI PMC

Murfuni I, Basile G, Subramanyam S, Malacaria E, Bignami M, Spies M, Franchitto A, Pichierri P. Survival of the replication checkpoint deficient cells requires MUS81-RAD52 function. PLoS Genet. 2013;9(10):e1003910. doi: 10.1371/journal.pgen.1003910. PubMed DOI PMC

Doe CL, Osman F, Dixon J, Whitby MC. DNA repair by a Rad22-Mus81-dependent pathway that is independent of Rhp51. Nucleic Acids Res. 2004;32(18):5570–81. doi: 10.1093/nar/gkh853. PubMed DOI PMC

Hanada K, Budzowska M, Modesti M, Maas A, Wyman C, Essers J, Kanaar R. The structure-specific endonuclease Mus81-Eme1 promotes conversion of interstrand DNA crosslinks into double-strands breaks. Embo J. 2006;25(20):4921–32. doi: 10.1038/sj.emboj.7601344. PubMed DOI PMC

Shimura T, Torres M, Martin M, Rao V, Pommier Y, Katsura M, Miyagawa K, Aladjerm M. Bloom's syndrome helicase and Mus81 are required to induce transient double-strand DNA breaks in response to DNA replication stress. J Mol Biol. 2008;375(4):1152–64. doi: 10.1016/j.jmb.2007.11.006. PubMed DOI PMC

Minocherhomji S, Ying S, Bjerregaard VA, Bursomanno S, Aleliunaite A, Wu W, Mankouri HW, Shen H, Liu Y, Hickson ID. Replication stress activates DNA repair synthesis in mitosis. Nature. 2015;528(7581):286–90. doi: 10.1038/nature16139. PubMed DOI

Bastin-Shanower S, Fricke W, Mullen J, Brill S. The mechanism of Mus81-Mms4 cleavage site selection distinguishes it from the homologous endonuclease Rad1-Rad10. Mol Cell Biol. 2003;23(10):3487–96. doi: 10.1128/MCB.23.10.3487-3496.2003. PubMed DOI PMC

Smith CE, Llorente B, Symington LS. Template switching during break-induced replication. Nature. 2007;447(7140):102–5. doi: 10.1038/nature05723. PubMed DOI

Mayle R, Campbell IM, Beck CR, Yu Y, Wilson M, Shaw CA, Bjergbaek L, Lupski JR, Ira G. DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage. Science. 2015;349(6249):742–7. doi: 10.1126/science.aaa8391. PubMed DOI PMC

Fu H, Martin MM, Regairaz M, Huang L, You Y, Lin CM, Ryan M, Kim R, Shimura T, Pommier Y, et al. The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage. Nat Commun. 2015;6:6746. doi: 10.1038/ncomms7746. PubMed DOI PMC

Tong A, Evangelista M, Parsons A, Xu H, Bader G, Page N, Robinson M, Raghibizadeh S, Hogue C, Bussey H, et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 2001;294(5550):2364–8. doi: 10.1126/science.1065810. PubMed DOI

Gomes X, Burgers P. ATP utilization by yeast replication factor C I. ATP-mediated interaction with DNA and with proliferating cell nuclear antigen. J Biol Chem. 2001;276(37):34768–75. doi: 10.1074/jbc.M011631200. PubMed DOI

Schmidt S, Pautz A, Burgers P. ATP utilization by yeast replication factor C IV. RFC ATP-binding mutants show defects in DNA replication, DNA repair, and checkpoint regulation. J Biol Chem. 2001;276(37):34792–800. doi: 10.1074/jbc.M011671200. PubMed DOI

Cullmann G, Fien K, Kobayashi R, Stillman B. Characterization of the five replication factor C genes of Saccharomyces cerevisiae. Mol Cell Biol. 1995;15(9):4661–71. doi: 10.1128/MCB.15.9.4661. PubMed DOI PMC

Schmidt S, Gomes X, Burgers P. ATP utilization by yeast replication factor C III. The ATP-binding domains of Rfc2, Rfc3, and Rfc4 are essential for DNA recognition and clamp loading. J Biol Chem. 2001;276(37):34784–91. doi: 10.1074/jbc.M011633200. PubMed DOI

Parnas O, Zipin-Roitman A, Pfander B, Liefshitz B, Mazor Y, Ben-Aroya S, Jentsch S, Kupiec M. Elg1, an alternative subunit of the RFC clamp loader, preferentially interacts with SUMOylated PCNA. EMBO J. 2010;29(15):2611–22. doi: 10.1038/emboj.2010.128. PubMed DOI PMC

Kubota T, Nishimura K, Kanemaki MT, Donaldson AD. The Elg1 replication factor C-like complex functions in PCNA unloading during DNA replication. Mol Cell. 2013;50(2):273–80. doi: 10.1016/j.molcel.2013.02.012. PubMed DOI

Kubota T, Katou Y, Nakato R, Shirahige K, Donaldson AD. Replication-coupled PCNA unloading by the Elg1 complex occurs genome-wide and requires Okazaki fragment ligation. Cell Rep. 2015;12(5):774–87. doi: 10.1016/j.celrep.2015.06.066. PubMed DOI PMC

Ben-Aroya S, Koren A, Liefshitz B, Steinlauf R, Kupiec M. ELG1, a novel yeast gene required for genome stability, forms a complex related to Replication Factor C. Yeast. 2003;20:S93. PubMed PMC

Hanada K, Budzowska M, Davies SL, van Drunen E, Onizawa H, Beverloo HB, Maas A, Essers J, Hickson ID, Kanaar R. The structure-specific endonuclease Mus81 contributes to replication restart by generating double-strand DNA breaks. Nat Struct Mol Biol. 2007;14(11):1096–104. doi: 10.1038/nsmb1313. PubMed DOI

Gomes XV, Burgers PM. Two modes of FEN1 binding to PCNA regulated by DNA. EMBO J. 2000;19(14):3811–21. doi: 10.1093/emboj/19.14.3811. PubMed DOI PMC

Vijayakumar S, Chapados BR, Schmidt KH, Kolodner RD, Tainer JA, Tomkinson AE. The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase. Nucleic Acids Res. 2007;35(5):1624–37. doi: 10.1093/nar/gkm006. PubMed DOI PMC

Cho I, Kim D, Kang Y, Lee C, Amangyelid T, Nguyen T, Hurwitz J, Seo Y. Human replication factor C stimulates flap endonuclease 1. J Biol Chem. 2009;284(16):10387–99. doi: 10.1074/jbc.M808893200. PubMed DOI PMC

Vasianovich Y, Altmannova V, Kotenko O, Newton MD, Krejci L, Makovets S. Unloading of homologous recombination factors is required for restoring double-stranded DNA at damage repair loci. EMBO J. 2017;36(2):213–31. doi: 10.15252/embj.201694628. PubMed DOI PMC

Kim Y, de la Torre A, Leal AA, Finkelstein IJ. Efficient modification of lambda-DNA substrates for single-molecule studies. Sci Rep. 2017;7(1):2071. doi: 10.1038/s41598-017-01984-x. PubMed DOI PMC

Mailand N, Gibbs-Seymour I, Bekker-Jensen S. Regulation of PCNA-protein interactions for genome stability. Nat Rev Mol Cell Biol. 2013;14(5):269–82. doi: 10.1038/nrm3562. PubMed DOI

Karras GI, Fumasoni M, Sienski G, Vanoli F, Branzei D, Jentsch S. Noncanonical role of the 9-1-1 clamp in the error-free DNA damage tolerance pathway. Mol Cell. 2013;49(3):536–46. doi: 10.1016/j.molcel.2012.11.016. PubMed DOI

Hutton RD, Roberts JA, Penedo JC, White MF. PCNA stimulates catalysis by structure-specific nucleases using two distinct mechanisms: substrate targeting and catalytic step. Nucleic Acids Res. 2008;36(21):6720–7. doi: 10.1093/nar/gkn745. PubMed DOI PMC

Zheng L, Dai H, Hegde ML, Zhou M, Guo Z, Wu X, Wu J, Su L, Zhong X, Mitra S, et al. Fen1 mutations that specifically disrupt its interaction with PCNA cause aneuploidy-associated cancer. Cell Res. 2011;21(7):1052–67. doi: 10.1038/cr.2011.35. PubMed DOI PMC

Bellaoui M, Chang M, Ou J, Xu H, Boone C, Brown GW. Elg1 forms an alternative RFC complex important for DNA replication and genome integrity. EMBO J. 2003;22(16):4304–13. doi: 10.1093/emboj/cdg406. PubMed DOI PMC

van Pel DM, Stirling PC, Minaker SW, Sipahimalani P, Hieter P. Saccharomyces cerevisiae genetics predicts candidate therapeutic genetic interactions at the mammalian replication fork. G3 (Bethesda) 2013;3(2):273–82. doi: 10.1534/g3.112.004754. PubMed DOI PMC

Saugar I, Vázquez MV, Gallo-Fernández M, Ortiz-Bazán M, Segurado M, Calzada A, Tercero JA. Temporal regulation of the Mus81-Mms4 endonuclease ensures cell survival under conditions of DNA damage. Nucleic Acids Res. 2013;41(19):8943–58. doi: 10.1093/nar/gkt645. PubMed DOI PMC

Interthal H, Heyer W. MUS81 encodes a novel Helix-hairpin-Helix protein involved in the response to UV- and methylation-induced DNA damage in Saccharomyces cerevisiae. Mol Gen Genet. 2000;263(5):812–27. doi: 10.1007/s004380000241. PubMed DOI

Mukherjee S, Wright WD, Ehmsen KT, Heyer WD. The Mus81-Mms4 structure-selective endonuclease requires nicked DNA junctions to undergo conformational changes and bend its DNA substrates for cleavage. Nucleic Acids Res. 2014;42(10):6511–22. doi: 10.1093/nar/gku265. PubMed DOI PMC

Gwon GH, Jo A, Baek K, Jin KS, Fu Y, Lee JB, Kim Y, Cho Y. Crystal structures of the structure-selective nuclease Mus81-Eme1 bound to flap DNA substrates. EMBO J. 2014;33(9):1061–72. doi: 10.1002/embj.201487820. PubMed DOI PMC

Tsutakawa SE, Classen S, Chapados BR, Arvai AS, Finger LD, Guenther G, Tomlinson CG, Thompson P, Sarker AH, Shen B, et al. Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily. Cell. 2011;145(2):198–211. doi: 10.1016/j.cell.2011.03.004. PubMed DOI PMC

Deem A, Keszthelyi A, Blackgrove T, Vayl A, Coffey B, Mathur R, Chabes A, Malkova A. Break-induced replication is highly inaccurate. PLoS Biol. 2011;9(2):e1000594. doi: 10.1371/journal.pbio.1000594. PubMed DOI PMC

Pardo B, Aguilera A. Complex chromosomal rearrangements mediated by break-induced replication involve structure-selective endonucleases. PLoS Genet. 2012;8(9):e1002979. doi: 10.1371/journal.pgen.1002979. PubMed DOI PMC

Stafa A, Donnianni RA, Timashev LA, Lam AF, Symington LS. Template switching during break-induced replication is promoted by the Mph1 helicase in Saccharomyces cerevisiae. Genetics. 2014;196(4):1017–28. doi: 10.1534/genetics.114.162297. PubMed DOI PMC

Lydeard JR, Lipkin-Moore Z, Sheu YJ, Stillman B, Burgers PM, Haber JE. Break-induced replication requires all essential DNA replication factors except those specific for pre-RC assembly. Genes Dev. 2010;24(11):1133–44. doi: 10.1101/gad.1922610. PubMed DOI PMC

Bartkova J, Horejsí Z, Koed K, Krämer A, Tort F, Zieger K, Guldberg P, Sehested M, Nesland JM, Lukas C, et al. DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis. Nature. 2005;434(7035):864–70. doi: 10.1038/nature03482. PubMed DOI

Zhao X, Muller EG, Rothstein R. A suppressor of two essential checkpoint genes identifies a novel protein that negatively affects dNTP pools. Mol Cell. 1998;2(3):329–40. doi: 10.1016/S1097-2765(00)80277-4. PubMed DOI

Thomas BJ, Rothstein R. Elevated recombination rates in transcriptionally active DNA. Cell. 1989;56(4):619–30. doi: 10.1016/0092-8674(89)90584-9. PubMed DOI

Sherman F. Getting started with yeast. Methods Enzymol. 1991;194:3–21. doi: 10.1016/0076-6879(91)94004-V. PubMed DOI

Sebesta M, Burkovics P, Haracska L, Krejci L. Reconstitution of DNA repair synthesis in vitro and the role of polymerase and helicase activities. DNA Repair. 2011;10(6):567–76. doi: 10.1016/j.dnarep.2011.03.003. PubMed DOI PMC

Shemesh K, Sebesta M, Pacesa M, Sau S, Bronstein A, Parnas O, Liefshitz B, Venclovas C, Krejci L, Kupiec M. A structure-function analysis of the yeast Elg1 protein reveals the importance of PCNA unloading in genome stability maintenance. Nucleic Acids Res. 2017;45(6):3189–203. PubMed PMC

Marini V, Krejci L. Unwinding of synthetic replication and recombination substrates by Srs2. DNA Repair (Amst) 2012;11(10):789–98. doi: 10.1016/j.dnarep.2012.05.007. PubMed DOI PMC

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