Sumoylation of the DNA polymerase ε by the Smc5/6 complex contributes to DNA replication
Autoři:
Xiangzhou Meng aff001; Lei Wei aff001; Xiao P. Peng aff001; Xiaolan Zhao aff001
Působiště autorů:
Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
aff001; Tri-Institutional MD-PhD Program of Weill Cornell Medical School, Rockefeller University, and Sloan-Kettering Cancer Center, New York, New York, United States of America
aff002
Vyšlo v časopise:
Sumoylation of the DNA polymerase ε by the Smc5/6 complex contributes to DNA replication. PLoS Genet 15(11): e32767. doi:10.1371/journal.pgen.1008426
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1008426
Souhrn
DNA polymerase epsilon (Pol ε) is critical for genome duplication, but little is known about how post-translational modification regulates its function. Here we report that the Pol ε catalytic subunit Pol2 in yeast is sumoylated at a single lysine within a catalytic domain insertion uniquely possessed by Pol2 family members. We found that Pol2 sumoylation occurs specifically in S phase and is increased under conditions of replication fork blockade. Analyses of the genetic requirements of this modification indicate that Pol2 sumoylation is associated with replication fork progression and dependent on the Smc5/6 SUMO ligase known to promote DNA synthesis. Consistently, the pol2 sumoylation mutant phenotype suggests impaired replication progression and increased levels of gross chromosomal rearrangements. Our findings thus indicate a direct role for SUMO in Pol2-mediated DNA synthesis and a molecular basis for Smc5/6-mediated regulation of genome stability.
Klíčová slova:
DNA replication – Telomeres – Protein domains – Lysine – Immunoprecipitation – DNA synthesis – Synthesis phase – SUMOylation
Zdroje
1. Hamatake RK, Hasegawa H, Clark AB, Bebenek K, Kunkel TA, Sugino A. Purification and characterization of DNA polymerase II from the yeast Saccharomyces cerevisiae. Identification of the catalytic core and a possible holoenzyme form of the enzyme. J Biol Chem. 1990;265(7):4072–83. 2406268
2. Morrison A, Araki H, Clark AB, Hamatake RK, Sugino A. A third essential DNA polymerase in S. cerevisiae. Cell. 1990;62(6):1143–51. doi: 10.1016/0092-8674(90)90391-q 2169349
3. Pursell ZF, Isoz I, Lundstrom EB, Johansson E, Kunkel TA. Yeast DNA polymerase ε participates in leading-strand DNA replication. Science. 2007;317(5834):127–30. doi: 10.1126/science.1144067 17615360
4. Tanaka S, Araki H. Helicase activation and establishment of replication forks at chromosomal origins of replication. Cold Spring Harb Perspect Biol. 2013;5(12):a010371.
5. Navas TA, Zhou Z, Elledge SJ. DNA polymerase epsilon links the DNA replication machinery to the S phase checkpoint. Cell. 1995;80(1):29–39. doi: 10.1016/0092-8674(95)90448-4 7813016
6. Yu C, Gan H, Serra-Cardona A, Zhang L, Gan S, Sharma S, et al. A mechanism for preventing asymmetric histone segregation onto replicating DNA strands. Science. 2018;361(6409):1386–9. doi: 10.1126/science.aat8849 30115745
7. Bellelli R, Belan O, Pye VE, Clement C, Maslen SL, Skehel JM, et al. POLE3-POLE4 is a histone H3-H4 chaperone that maintains chromatin integrity during DNA replication. Mol Cell. 2018;72(1):112–26.e5. doi: 10.1016/j.molcel.2018.08.043 30217558
8. Cremona CA, Sarangi P, Yang Y, Hang LE, Rahman S, Zhao X. Extensive DNA damage-induced sumoylation contributes to replication and repair and acts in addition to the Mec1 checkpoint. Mol Cell. 2012;45(3):422–332. doi: 10.1016/j.molcel.2011.11.028 22285753
9. Johnson ES. Protein modification by SUMO. Annu Rev Biochem. 2004;73:355–82. doi: 10.1146/annurev.biochem.73.011303.074118 15189146
10. Hickey CM, Wilson NR, Hochstrasser M. Function and regulation of SUMO proteases. Nat Rev Mol Cell Biol. 2012;13(12):755–66. doi: 10.1038/nrm3478 23175280
11. Zhao X. SUMO-mediated regulation of nuclear functions and signaling processes. Mol Cell. 2018;71(3):409–18. doi: 10.1016/j.molcel.2018.07.027 30075142
12. Zhao X, Blobel G. A SUMO ligase is part of a nuclear multiprotein complex that affects DNA repair and chromosomal organization. Proc Natl Acad Sci USA. 2005;102(13):4777–82. doi: 10.1073/pnas.0500537102 15738391
13. Johnson ES, Gupta AA. An E3-like factor that promotes SUMO conjugation to the yeast septins. Cell. 2001;106(6):735–44. doi: 10.1016/s0092-8674(01)00491-3 11572779
14. Payne F, Colnaghi R, Rocha N, Seth A, Harris J, Carpenter G, et al. Hypomorphism in human NSMCE2 linked to primordial dwarfism and insulin resistance. J Clin Invest. 2014;124(9):4028–38. doi: 10.1172/JCI73264 25105364
15. van der Crabben SN, Hennus MP, McGregor GA, Ritter DI, Nagamani SC, Wells OS, et al. Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease. J Clin Invest. 2016;126(8):2881–92. doi: 10.1172/JCI82890 27427983
16. Wei L, Zhao X. Roles of SUMO in replication initiation, progression, and termination. Adv Exp Med Biol. 2017;1042:371–93. doi: 10.1007/978-981-10-6955-0_17 29357067
17. Papouli E, Chen S, Davies AA, Huttner D, Krejci L, Sung P, et al. Crosstalk between SUMO and ubiquitin on PCNA is mediated by recruitment of the helicase Srs2p. Mol Cell. 2005;19(1):123–33. doi: 10.1016/j.molcel.2005.06.001 15989970
18. Pfander B, Moldovan GL, Sacher M, Hoege C, Jentsch S. SUMO-modified PCNA recruits Srs2 to prevent recombination during S phase. Nature. 2005;436(7049):428–33. doi: 10.1038/nature03665 15931174
19. Wei L, Zhao X. A new MCM modification cycle regulates DNA replication initiation. Nat Struct Mol Biol. 2016;23(3):209–16. doi: 10.1038/nsmb.3173 26854664
20. Hendriks IA, D'Souza RC, Yang B, Verlaan-de Vries M, Mann M, Vertegaal AC. Uncovering global SUMOylation signaling networks in a site-specific manner. Nat Struct Mol Biol. 2014;21(10):927–36. doi: 10.1038/nsmb.2890 25218447
21. Sampson DA, Wang M, Matunis MJ. The small ubiquitin-like modifier-1 (SUMO-1) consensus sequence mediates Ubc9 binding and is essential for SUMO-1 modification. J Biol Chem. 2001;276(24):21664–9. doi: 10.1074/jbc.M100006200 11259410
22. Rodriguez MS, Dargemont C, Hay RT. SUMO-1 conjugation in vivo requires both a consensus modification motif and nuclear targeting. J Biol Chem. 2001;276(16):12654–9. doi: 10.1074/jbc.M009476200 11124955
23. Johansson E, Dixon N. Replicative DNA polymerases. Cold Spring Harb Symp Quant Biol. 2013;5(6):a012799.
24. Hogg M, Osterman P, Bylund GO, Ganai RA, Lundström E-B, Sauer-Eriksson AE, et al. Structural basis for processive DNA synthesis by yeast DNA polymerase ɛ. Nat Struct Mol Biol. 2014;21:49–55. doi: 10.1038/nsmb.2712 24292646
25. Aragon L. The Smc5/6 Complex: new and old functions of the enigmatic long-distance relative. Annu Rev Genet. 2018;52:89–107. doi: 10.1146/annurev-genet-120417-031353 30476445
26. Friedel AM, Pike BL, Gasser SM. ATR/Mec1: coordinating fork stability and repair. Curr Opin Cell Biol. 2009;21(2):237–44. doi: 10.1016/j.ceb.2009.01.017 19230642
27. 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 9774971
28. Ohya T, Maki S, Kawasaki Y, Sugino A. Structure and function of the fourth subunit (Dpb4p) of DNA polymerase epsilon in Saccharomyces cerevisiae. Nucleic Acids Res. 2000;28(20):3846–52. doi: 10.1093/nar/28.20.3846 11024162
29. Aksenova A, Volkov K, Maceluch J, Pursell ZF, Rogozin IB, Kunkel TA, et al. Mismatch repair-independent increase in spontaneous mutagenesis in yeast lacking non-essential subunits of DNA polymerase ε. PLoS Genet. 2010;6(11):e1001209. doi: 10.1371/journal.pgen.1001209 21124948
30. Ivessa AS, Lenzmeier BA, Bessler JB, Goudsouzian LK, Schnakenberg SL, Zakian VA. The Saccharomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes. Mol Cell. 2003;12(6):1525–36. doi: 10.1016/s1097-2765(03)00456-8 14690605
31. Yeeles JTP, Janska A, Early A, Diffley JFX. How the eukaryotic replisome achieves rapid and efficient DNA replication. Mol Cell. 2017;65:105–16. doi: 10.1016/j.molcel.2016.11.017 27989442
32. Araki H, Hamatake RK, Johnston LH, Sugino A. DPB2, the gene encoding DNA polymerase II subunit B, is required for chromosome replication in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1991;88(11):4601–5. doi: 10.1073/pnas.88.11.4601 2052544
33. Isoz I, Persson U, Volkov K, Johansson E. The C-terminus of Dpb2 is required for interaction with Pol2 and for cell viability. Nucleic Acids Res. 2012;40(22):11545–53. doi: 10.1093/nar/gks880 23034803
34. Dua R, Levy DL, Campbell JL. 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. 1998;273(45):30046–55. doi: 10.1074/jbc.273.45.30046 9792727
35. Wahba L, Costantino L, Tan FJ, Zimmer A, Koshland D. S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation. Genes Dev. 2016;30(11):1327–38. doi: 10.1101/gad.280834.116 27298336
36. Fachinetti D, Bermejo R, Cocito A, Minardi S, Katou Y, Kanoh Y, et al. Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements. Mol Cell. 2010;39(4):595–605. doi: 10.1016/j.molcel.2010.07.024 20797631
37. Wellinger RJ, Zakian VA. Everything you ever wanted to know about Saccharomyces cerevisiae telomeres: beginning to end. Genetics. 2012;191(4):1073–105. doi: 10.1534/genetics.111.137851 22879408
38. Balk B, Maicher A, Dees M, Klermund J, Luke-Glaser S, Bender K, et al. Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence. Nat Struct Mol Biol. 2013;20(10):1199–205. doi: 10.1038/nsmb.2662 24013207
39. Pfeiffer V, Crittin J, Grolimund L, Lingner J. The THO complex component Thp2 counteracts telomeric R-loops and telomere shortening. EMBO J. 2013;32(21):2861–71. doi: 10.1038/emboj.2013.217 24084588
40. El Hage A, French SL, Beyer AL, Tollervey D. Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev. 2010;24(14):1546–58. doi: 10.1101/gad.573310 20634320
41. Ribeyre C, Zellweger R, Chauvin M, Bec N, Larroque C, Lopes M, et al. Nascent DNA proteomics reveals a chromatin remodeler required for Topoisomerase I loading at replication forks. Cell Rep. 2016;15(2):300–9. doi: 10.1016/j.celrep.2016.03.027 27050524
42. Marinello J, Chillemi G, Bueno S, Manzo SG, Capranico G. Antisense transcripts enhanced by camptothecin at divergent CpG-island promoters associated with bursts of topoisomerase I-DNA cleavage complex and R-loop formation. Nucleic Acids Res. 2013;41(22):10110–23. doi: 10.1093/nar/gkt778 23999093
43. Aguilera A, Gomez-Gonzalez B. DNA-RNA hybrids: the risks of DNA breakage during transcription. Nat Struct Mol Biol. 2017;24(5):439–43. doi: 10.1038/nsmb.3395 28471430
44. Chen YH, Choi K, Szakal B, Arenz J, Duan XY, Ye H, et al. Interplay between the Smc5/6 complex and the Mph1 helicase in recombinational repair. Proc Natl Acad Sci USA. 2009;106(50):21252–7. doi: 10.1073/pnas.0908258106 19995966
45. Putnam CD, Srivatsan A, Nene RV, Martinez SL, Clotfelter SP, Bell SN, et al. A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers. Nat Commun. 2016;7:11256. doi: 10.1038/ncomms11256 27071721
46. Torres-Rosell J, De Piccoli G, Cordon-Preciado V, Farmer S, Jarmuz A, Machin F, et al. Anaphase onset before complete DNA replication with intact checkpoint responses. Science. 2007;315(5817):1411–5. doi: 10.1126/science.1134025 17347440
47. Sarangi P, Zhao X. SUMO-mediated regulation of DNA damage repair and responses. Trends Biochem Sci. 2015;40(4):233–42. doi: 10.1016/j.tibs.2015.02.006 25778614
48. Zhao X, Rothstein R. The Dun1 checkpoint kinase phosphorylates and regulates the ribonucleotide reductase inhibitor Sml1. Proc Natl Acad Sci U S A. 2002;99(6):3746–51. doi: 10.1073/pnas.062502299 11904430
49. Peng XP, Lim S, Li S, Marjavaara L, Chabes A, Zhao X. Acute Smc5/6 depletion reveals its primary role in rDNA replication by restraining recombination at fork pausing sites. PLoS Genet. 2018;14(1):e1007129. doi: 10.1371/journal.pgen.1007129 29360860
50. Putnam CD, Kolodner RD. Determination of gross chromosomal rearrangement rates. Cold Spring Harb Protoc. 2010;2010(9):pdb.prot5492.
51. Wan B, Wu J, Meng X, Lei M, Zhao X. Molecular basis for control of diverse genome stability factors by the multi-BRCT scaffold Rtt107. Mol Cell. 2019;75(2):238–51.e5. doi: 10.1016/j.molcel.2019.05.035 31348879
52. Myung K, Smith S, Kolodner RD. Mitotic checkpoint function in the formation of gross chromosomal rearrangements in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2004;101(45):15980–5. doi: 10.1073/pnas.0407010101 15514023
53. Okita AK, Zafar F, Su J, Weerasekara D, Kajitani T, Takahashi TS, et al. Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription. Commun Biol. 2019;2:17. doi: 10.1038/s42003-018-0251-z 30652128
54. Hang LE, Liu X, Cheung I, Yang Y, Zhao X. SUMOylation regulates telomere length homeostasis by targeting Cdc13. Nat Struct Mol Biol. 2011;18(8):1–8.
55. Gohring J, Fulcher N, Jacak J, Riha K. TeloTool: a new tool for telomere length measurement from terminal restriction fragment analysis with improved probe intensity correction. Nucleic Acids Res. 2014;42(3):e21. doi: 10.1093/nar/gkt1315 24366880
56. Tanaka S, Miyazawa-Onami M, Iida T, Araki H. iAID: an improved auxin-inducible degron system for the construction of a ‘tight’ conditional mutant in the budding yeast Saccharomyces cerevisiae. Yeast. 2015;32(8):567–81. doi: 10.1002/yea.3080 26081484
57. Symington LS, Rothstein R, Lisby M. Mechanisms and regulation of mitotic recombination in Saccharomyces cerevisiae. Genetics. 2014;198(3):795–835. doi: 10.1534/genetics.114.166140 25381364
58. Putnam CD, Hayes TK, Kolodner RD. Specific pathways prevent duplication-mediated genome rearrangements. Nature. 2009;460(7258):984–9. doi: 10.1038/nature08217 19641493
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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