Sumoylation influences DNA break repair partly by increasing the solubility of a conserved end resection protein

. 2015 Jan ; 11 (1) : e1004899. [epub] 20150108

Jazyk angličtina Země Spojené státy americké Médium electronic-ecollection

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid25569253

Grantová podpora
Wellcome Trust - United Kingdom
P30 CA008748 NCI NIH HHS - United States
R01 GM080670 NIGMS NIH HHS - United States
GM080670 NIGMS NIH HHS - United States

Odkazy

PubMed 25569253
PubMed Central PMC4287433
DOI 10.1371/journal.pgen.1004899
PII: PGENETICS-D-14-01771
Knihovny.cz E-zdroje

Protein modifications regulate both DNA repair levels and pathway choice. How each modification achieves regulatory effects and how different modifications collaborate with each other are important questions to be answered. Here, we show that sumoylation regulates double-strand break repair partly by modifying the end resection factor Sae2. This modification is conserved from yeast to humans, and is induced by DNA damage. We mapped the sumoylation site of Sae2 to a single lysine in its self-association domain. Abolishing Sae2 sumoylation by mutating this lysine to arginine impaired Sae2 function in the processing and repair of multiple types of DNA breaks. We found that Sae2 sumoylation occurs independently of its phosphorylation, and the two modifications act in synergy to increase soluble forms of Sae2. We also provide evidence that sumoylation of the Sae2-binding nuclease, the Mre11-Rad50-Xrs2 complex, further increases end resection. These findings reveal a novel role for sumoylation in DNA repair by regulating the solubility of an end resection factor. They also show that collaboration between different modifications and among multiple substrates leads to a stronger biological effect.

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Ciccia A, Elledge SJ (2010) The DNA damage response: making it safe to play with knives. Mol Cell 40: 179–204. PubMed PMC

Marechal A, Zou L (2013) DNA damage sensing by the ATM and ATR kinases. Cold Spring Harb Perspect Biol 5. PubMed PMC

Polo SE, Jackson SP (2011) Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications. Genes Dev 25: 409–433. PubMed PMC

Symington LS, Gautier J (2011) Double-strand break end resection and repair pathway choice. Annu Rev Genet 45: 247–271. PubMed

Chapman JR, Taylor MR, Boulton SJ (2012) Playing the end game: DNA double-strand break repair pathway choice. Mol Cell 47: 497–510. PubMed

Herzberg K, Bashkirov VI, Rolfsmeier M, Haghnazari E, McDonald WH, et al. (2006) Phosphorylation of Rad55 on serines 2, 8, and 14 is required for efficient homologous recombination in the recovery of stalled replication forks. Mol Cell Biol 26: 8396–8409. PubMed PMC

Smolka MB, Albuquerque CP, Chen SH, Zhou H (2007) Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc Natl Acad Sci USA 104: 10364–10369. PubMed PMC

Chen X, Niu H, Chung WH, Zhu Z, Papusha A, et al. (2011) Cell cycle regulation of DNA double-strand break end resection by Cdk1-dependent Dna2 phosphorylation. Nat Struct Mol Biol 18: 1015–1019. PubMed PMC

Matos J, Blanco MG, Maslen S, Skehel JM, West SC (2011) Regulatory control of the resolution of DNA recombination intermediates during meiosis and mitosis. Cell 147: 158–172. PubMed PMC

Cremona CA, Sarangi P, Zhao X (2012) Sumoylation and the DNA Damage Response. Biomolecules 2: 376–388. PubMed PMC

Jackson SP, Durocher D (2013) Regulation of DNA damage responses by ubiquitin and SUMO. Mol Cell 49: 795–807. PubMed

Ulrich HD (2014) Two-way communications between ubiquitin-like modifiers and DNA. Nat Struct Mol Biol 21: 317–324. PubMed

Jentsch S, Psakhye I (2013) Control of nuclear activities by substrate-selective and protein-group SUMOylation. Annu Rev Genet 47: 167–186. PubMed

Maeda D, Seki M, Onoda F, Branzei D, Kawabe Y, et al. (2004) Ubc9 is required for damage-tolerance and damage-induced interchromosomal homologous recombination in S. cerevisiae . DNA Repair 3: 335–341. PubMed

Morris JR, Boutell C, Keppler M, Densham R, Weekes D, et al. (2009) The SUMO modification pathway is involved in the BRCA1 response to genotoxic stress. Nature 462: 886–890. PubMed

Galanty Y, Belotserkovskaya R, Coates J, Polo S, Miller KM, et al. (2009) Mammalian SUMO E3-ligases PIAS1 and PIAS4 promote responses to DNA double-strand breaks. Nature 462: 935–939. PubMed PMC

Cremona CA, Sarangi P, Yang Y, Hang LE, Rahman S, et al. (2012) Extensive DNA damage-induced sumoylation contributes to replication and repair and acts in addition to the Mec1 checkpoint. Mol Cell 45: 422–432. PubMed PMC

Psakhye I, Jentsch S (2012) Protein group modification and synergy in the SUMO pathway as exemplified in DNA repair. Cell 151: 807–820. PubMed

Paull TT (2010) Making the best of the loose ends: Mre11/Rad50 complexes and Sae2 promote DNA double-strand break resection. DNA Repair (Amst) 9: 1283–1291. PubMed PMC

Mimitou EP, Symington LS (2011) DNA end resection–unraveling the tail. DNA Repair (Amst) 10: 344–348. PubMed PMC

Lengsfeld BM, Rattray AJ, Bhaskara V, Ghirlando R, Paull TT (2007) Sae2 is an endonuclease that processes hairpin DNA cooperatively with the Mre11/Rad50/Xrs2 complex. Mol Cell 28: 638–651. PubMed PMC

Mimitou EP, Symington LS (2008) Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing. Nature 455: 770–774. PubMed PMC

Clerici M, Mantiero D, Lucchini G, Longhese MP (2005) The Saccharomyces cerevisiae Sae2 protein promotes resection and bridging of double strand break ends. J Biol Chem 280: 38631–38638. PubMed

Zhu Z, Chung WH, Shim EY, Lee SE, Ira G (2008) Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends. Cell 134: 981–994. PubMed PMC

Nicolette ML, Lee K, Guo Z, Rani M, Chow JM, et al. (2010) Mre11-Rad50-Xrs2 and Sae2 promote 5′ strand resection of DNA double-strand breaks. Nat Struct Mol Biol 17: 1478–1485. PubMed PMC

Cannavo E, Cejka P (2014) Sae2 promotes dsDNA endonuclease activity within Mre11-Rad50-Xrs2 to resect DNA breaks. Nature 514: 122–125. PubMed

Lobachev KS, Gordenin DA, Resnick MA (2002) The Mre11 complex is required for repair of hairpin-capped double-strand breaks and prevention of chromosome rearrangements. Cell 108: 183–193. PubMed

Neale MJ, Pan J, Keeney S (2005) Endonucleolytic processing of covalent protein-linked DNA double-strand breaks. Nature 436: 1053–1057. PubMed PMC

Deng C, Brown JA, You D, Brown JM (2005) Multiple endonucleases function to repair covalent topoisomerase I complexes in Saccharomyces cerevisiae . Genetics 170: 591–600. PubMed PMC

Zierhut C, Diffley JF (2008) Break dosage, cell cycle stage and DNA replication influence DNA double strand break response. EMBO J 27: 1875–1885. PubMed PMC

Ira G, Pellicioli A, Balijja A, Wang X, Fiorani S, et al. (2004) DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1. Nature 431: 1011–1017. PubMed PMC

Aylon Y, Liefshitz B, Kupiec M (2004) The CDK regulates repair of double-strand breaks by homologous recombination during the cell cycle. EMBO J 23: 4868–4875. PubMed PMC

Baroni E, Viscardi V, Cartagena-Lirola H, Lucchini G, Longhese MP (2004) The functions of budding yeast Sae2 in the DNA damage response require Mec1- and Tel1-dependent phosphorylation. Mol Cell Biol 24: 4151–4165. PubMed PMC

Falck J, Forment JV, Coates J, Mistrik M, Lukas J, et al. (2012) CDK targeting of NBS1 promotes DNA-end resection, replication restart and homologous recombination. EMBO Rep 13: 561–568. PubMed PMC

Zhang Y, Shim EY, Davis M, Lee SE (2009) Regulation of repair choice: Cdk1 suppresses recruitment of end joining factors at DNA breaks. DNA Repair (Amst) 8: 1235–1241. PubMed PMC

Huertas P, Cortes-Ledesma F, Sartori AA, Aguilera A, Jackson SP (2008) CDK targets Sae2 to control DNA-end resection and homologous recombination. Nature 455: 689–692. PubMed PMC

Fu Q, Chow J, Bernstein KA, Makharashvili N, Arora S, et al. (2014) Phosphorylation-regulated transitions in an oligomeric state control the activity of the Sae2 DNA repair enzyme. Mol Cell Biol 34: 778–793. PubMed PMC

Rodriguez MS, Dargemont C, Hay RT (2001) SUMO-1 conjugation in vivo requires both a consensus modification motif and nuclear targeting. J Biol Chem 276: 12654–12659. PubMed

Sampson DA, Wang M, Matunis MJ (2001) The small ubiquitin-like modifier-1 (SUMO-1) consensus sequence mediates Ubc9 binding and is essential for SUMO-1 modification. J Biol Chem 276: 21664–21669. PubMed

Dubin MJ, Stokes PH, Sum EY, Williams RS, Valova VA, et al. (2004) Dimerization of CtIP, a BRCA1- and CtBP-interacting protein, is mediated by an N-terminal coiled-coil motif. J Biol Chem 279: 26932–26938. PubMed

Kim HS, Vijayakumar S, Reger M, Harrison JC, Haber JE, et al. (2008) Functional interactions between Sae2 and the Mre11 complex. Genetics 178: 711–723. PubMed PMC

You Z, Shi LZ, Zhu Q, Wu P, Zhang YW, et al. (2009) CtIP links DNA double-strand break sensing to resection. Mol Cell 36: 954–969. PubMed PMC

Lobachev KS, Stenger JE, Kozyreva OG, Jurka J, Gordenin DA, et al. (2000) Inverted Alu repeats unstable in yeast are excluded from the human genome. EMBO J 19: 3822–3830. PubMed PMC

Foster SS, Balestrini A, Petrini JH (2011) Functional interplay of the Mre11 nuclease and Ku in the response to replication-associated DNA damage. Mol Cell Biol 31: 4379–4389. PubMed PMC

Prinz S, Amon A, Klein F (1997) Isolation of COM1, a new gene required to complete meiotic double-strand break-induced recombination in Saccharomyces cerevisiae . Genetics 146: 781–795. PubMed PMC

Keeney S, Kleckner N (1995) Covalent protein-DNA complexes at the 5′ strand termini of meiosis-specific double-strand breaks in yeast. Proc Natl Acad Sci USA 92: 11274–11278. PubMed PMC

McKee AH, Kleckner N (1997) A general method for identifying recessive diploid-specific mutations in Saccharomyces cerevisiae, its application to the isolation of mutants blocked at intermediate stages of meiotic prophase and characterization of a new gene SAE2 . Genetics 146: 797–816. PubMed PMC

Chen H, Lisby M, Symington LS (2013) RPA coordinates DNA end resection and prevents formation of DNA hairpins. Mol Cell 50: 589–600. PubMed PMC

Lee K, Lee SE (2007) Saccharomyces cerevisiae Sae2- and Tel1-dependent single-strand DNA formation at DNA break promotes microhomology-mediated end joining. Genetics 176: 2003–2014. PubMed PMC

Deng SK, Gibb B, de Almeida MJ, Greene EC, Symington LS (2014) RPA antagonizes microhomology-mediated repair of DNA double-strand breaks. Nat Struct Mol Biol 21: 405–412. PubMed PMC

Boulton SJ, Jackson SP (1996) Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone DNA repair pathways. EMBO J 15: 5093–5103. PubMed PMC

Almedawar S, Colomina N, Bermudez-Lopez M, Pocino-Merino I, Torres-Rosell J (2012) A SUMO-dependent step during establishment of sister chromatid cohesion. Curr Biol 22: 1576–1581. PubMed

Wu D, Topper LM, Wilson TE (2008) Recruitment and dissociation of nonhomologous end joining proteins at a DNA double-strand break in Saccharomyces cerevisiae . Genetics 178: 1237–1249. PubMed PMC

Palmbos PL, Daley JM, Wilson TE (2005) Mutations of the Yku80 C terminus and Xrs2 FHA domain specifically block yeast nonhomologous end joining. Mol Cell Biol 25: 10782–10790. PubMed PMC

Lisby M, Barlow JH, Burgess RC, Rothstein R (2004) Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins. Cell 118: 699–713. PubMed

Mimitou EP, Symington LS (2010) Ku prevents Exo1 and Sgs1-dependent resection of DNA ends in the absence of a functional MRX complex or Sae2. EMBO J 29: 3358–3369. PubMed PMC

Hang LE, Lopez CR, Liu X, Williams JM, Chung I, et al. (2014) Regulation of Ku-DNA association by Yku70 C-terminal tail and SUMO modification. J Biol Chem PubMed PMC

Li F, Dong J, Pan X, Oum JH, Boeke JD, et al. (2008) Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates. Mol Cell 30: 325–335. PubMed PMC

Guzder SN, Sommers CH, Prakash L, Prakash S (2006) Complex formation with damage recognition protein Rad14 is essential for Saccharomyces cerevisiae Rad1-Rad10 nuclease to perform its function in nucleotide excision repair in vivo . Mol Cell Biol 26: 1135–1141. PubMed PMC

Toh GW, Sugawara N, Dong J, Toth R, Lee SE, et al. (2010) Mec1/Tel1-dependent phosphorylation of Slx4 stimulates Rad1-Rad10-dependent cleavage of non-homologous DNA tails. DNA Repair 9: 718–726. PubMed PMC

Shim EY, Chung WH, Nicolette ML, Zhang Y, Davis M, et al. (2010) Saccharomyces cerevisiae Mre11/Rad50/Xrs2 and Ku proteins regulate association of Exo1 and Dna2 with DNA breaks. Embo J 29: 3370–3380. PubMed PMC

Robert T, Vanoli F, Chiolo I, Shubassi G, Bernstein KA, et al. (2011) HDACs link the DNA damage response, processing of double-strand breaks and autophagy. Nature 471: 74–79. PubMed PMC

Lafranchi L, de Boer HR, de Vries EG, Ong SE, Sartori AA, et al. (2014) APC/CCdh1 controls CtIP stability during the cell cycle and in response to DNA damage. EMBO J PubMed PMC

Steffan JS, Agrawal N, Pallos J, Rockabrand E, Trotman LC, et al. (2004) SUMO modification of Huntingtin and Huntington's disease pathology. Science 304: 100–104. PubMed

Janer A, Werner A, Takahashi-Fujigasaki J, Daret A, Fujigasaki H, et al. (2010) SUMOylation attenuates the aggregation propensity and cellular toxicity of the polyglutamine expanded ataxin-7. Hum Mol Genet 19: 181–195. PubMed

Krumova P, Meulmeester E, Garrido M, Tirard M, Hsiao HH, et al. (2011) Sumoylation inhibits alpha-synuclein aggregation and toxicity. J Cell Biol 194: 49–60. PubMed PMC

Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L (2004) Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 22: 1302–1306. PubMed

Pawar AP, Dubay KF, Zurdo J, Chiti F, Vendruscolo M, et al. (2005) Prediction of “aggregation-prone” and “aggregation-susceptible” regions in proteins associated with neurodegenerative diseases. J Mol Biol 350: 379–392. PubMed

Zuo X, Li S, Hall J, Mattern MR, Tran H, et al. (2005) Enhanced expression and purification of membrane proteins by SUMO fusion in Escherichia coli . J Struct Funct Genomics 6: 103–111. PubMed PMC

Malakhov MP, Mattern MR, Malakhova OA, Drinker M, Weeks SD, et al. (2004) SUMO fusions and SUMO-specific protease for efficient expression and purification of proteins. J Struct Funct Genomics 5: 75–86. PubMed

Lin DY, Huang YS, Jeng JC, Kuo HY, Chang CC, et al. (2006) Role of SUMO-interacting motif in Daxx SUMO modification, subnuclear localization, and repression of sumoylated transcription factors. Mol Cell 24: 341–354. PubMed

Shen TH, Lin HK, Scaglioni PP, Yung TM, Pandolfi PP (2006) The mechanisms of PML-nuclear body formation. Mol Cell 24: 331–339. PubMed PMC

Conchillo-Sole O, de Groot NS, Aviles FX, Vendrell J, Daura X, et al. (2007) AGGRESCAN: a server for the prediction and evaluation of “hot spots” of aggregation in polypeptides. BMC Bioinformatics 8: 65. PubMed PMC

Silver HR, Nissley JA, Reed SH, Hou YM, Johnson ES (2011) A role for SUMO in nucleotide excision repair. DNA Repair 10: 1243–1251. PubMed PMC

Sarangi P, Bartosova Z, Altmannova V, Holland C, Chavdarova M, et al. (2014) Sumoylation of the Rad1 nuclease promotes DNA repair and regulates its DNA association. Nucleic Acids Res 42: 6393–6404. PubMed PMC

Sarangi P, Altmannova V, Holland C, Bartosova Z, Hao F, et al. (2014) A Versatile Scaffold Contributes to Damage Survival via Sumoylation and Nuclease Interactions. Cell Rep 9: 143–152. PubMed PMC

Sacher M, Pfander B, Hoege C, Jentsch S (2006) Control of Rad52 recombination activity by double-strand break-induced SUMO modification. Nat Cell Biol 8: 1284–1290. PubMed

Tomimatsu N, Mukherjee B, Catherine Hardebeck M, Ilcheva M, Vanessa Camacho C, et al. (2014) Phosphorylation of Exo1 by CDKs 1 and 2 regulates DNA end resection and repair pathway choice. Nat Commun 5: 3561. PubMed PMC

Gallo-Fernandez M, Saugar I, Ortiz-Bazan MA, Vazquez MV, Tercero JA (2012) Cell cycle-dependent regulation of the nuclease activity of Mus81-Eme1/Mms4. Nucleic Acids Res 40: 8325–8335. PubMed PMC

Morin I, Ngo HP, Greenall A, Zubko MK, Morrice N, et al. (2008) Checkpoint-dependent phosphorylation of Exo1 modulates the DNA damage response. EMBO J 27: 2400–2410. PubMed PMC

Burgess RC, Rahman S, Lisby M, Rothstein R, Zhao X (2007) The Slx5-Slx8 complex affects sumoylation of DNA repair proteins and negatively regulates recombination. Mol Cell Biol 27: 6153–6162. PubMed PMC

Tsalik EL, Gartenberg MR (1998) Curing Saccharomyces cerevisiae of the 2 micron plasmid by targeted DNA damage. Yeast 14: 847–852. PubMed

Zhao X, Blobel G (2005) A SUMO ligase is part of a nuclear multiprotein complex that affects DNA repair and chromosomal organization. Proc Natl Acad Sci USA 102: 4777–4782. PubMed PMC

Uchimura Y, Nakamura M, Sugasawa K, Nakao M, Saitoh H (2004) Overproduction of eukaryotic SUMO-1- and SUMO-2-conjugated proteins in Escherichia coli . Anal Biochem 331: 204–206. PubMed

Sartori AA, Lukas C, Coates J, Mistrik M, Fu S, et al. (2007) Human CtIP promotes DNA end resection. Nature 450: 509–514. PubMed PMC

Mossessova E, Lima CD (2000) Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol Cell 5: 865–876. PubMed

Moore JK, Haber JE (1996) Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae . Mol Cell Biol 16: 2164–2173. PubMed PMC

Zhao X, Muller EG, Rothstein R (1998) A suppressor of two essential checkpoint genes identifies a novel protein that negatively affects dNTP pools. Mol Cell 2: 329–340. PubMed

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