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Checkpoint Activation of an Unconventional DNA Replication Program in


DNA damage and replication stress activate cell cycle checkpoint responses that protect the integrity of eukaryotic chromosomes. A well-conserved response involves the reversible phosphorylation of the replicative helicase, MCM2-7, which together with the origin recognition complex (ORC) dictates when and where replication initiates in chromosomes. The central role of ORC and MCMs in DNA replication is illustrated by the fact that small changes in abundance of these pre-replicative complex (pre-RC) components are poorly tolerated from yeast to humans. Here we describe an unprecedented replication stress checkpoint response in the early branching eukaryote, Tetrahymena thermophila, that is triggered by the depletion of dNTP pools with hydroxyurea (HU). Instead of transiently phosphorylating MCM subunits, ORC and MCM proteins are physically degraded in HU-treated Tetrahymena. Unexpectedly, upon HU removal the genome is completely and effortlessly replicated prior to replenishment of ORC and MCM components. Using DNA fiber imaging and 2D gel electrophoresis, we show that ORC-dependent mechanisms are bypassed during the recovery phase to produce bidirectional replication forks throughout the genome. Our findings suggest that Tetrahymena enlists an alternative mechanism for replication initiation, and that the underlying process can operate on a genome-wide scale.


Vyšlo v časopise: Checkpoint Activation of an Unconventional DNA Replication Program in. PLoS Genet 11(7): e32767. doi:10.1371/journal.pgen.1005405
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005405

Souhrn

DNA damage and replication stress activate cell cycle checkpoint responses that protect the integrity of eukaryotic chromosomes. A well-conserved response involves the reversible phosphorylation of the replicative helicase, MCM2-7, which together with the origin recognition complex (ORC) dictates when and where replication initiates in chromosomes. The central role of ORC and MCMs in DNA replication is illustrated by the fact that small changes in abundance of these pre-replicative complex (pre-RC) components are poorly tolerated from yeast to humans. Here we describe an unprecedented replication stress checkpoint response in the early branching eukaryote, Tetrahymena thermophila, that is triggered by the depletion of dNTP pools with hydroxyurea (HU). Instead of transiently phosphorylating MCM subunits, ORC and MCM proteins are physically degraded in HU-treated Tetrahymena. Unexpectedly, upon HU removal the genome is completely and effortlessly replicated prior to replenishment of ORC and MCM components. Using DNA fiber imaging and 2D gel electrophoresis, we show that ORC-dependent mechanisms are bypassed during the recovery phase to produce bidirectional replication forks throughout the genome. Our findings suggest that Tetrahymena enlists an alternative mechanism for replication initiation, and that the underlying process can operate on a genome-wide scale.


Zdroje

1. Cimprich KA, Cortez D. ATR: an essential regulator of genome integrity. Nat Rev Mol Cell Biol. 2008;9: 616–627. doi: 10.1038/nrm2450 18594563

2. Cortez D, Glick G, Elledge SJ. Minichromosome maintenance proteins are direct targets of the ATM and ATR checkpoint kinases. Proc Natl Acad Sci USA. 2004;101: 10078–10083. 15210935

3. Randell JCW, Fan A, Chan C, Francis LI, Heller RC, Galani K, et al. Mec1 is one of multiple kinases that prime the Mcm2-7 helicase for phosphorylation by Cdc7. Mol Cell. 2010;40: 353–363. doi: 10.1016/j.molcel.2010.10.017 21070963

4. Snaith HA, Brown GW, Forsburg SL. Schizosaccharomyces pombe Hsk1p is a potential cds1p target required for genome integrity. Mol Cell Biol. 2000;20: 7922–7932. 11027263

5. Levenson V, Hamlin JL. A general protocol for evaluating the specific effects of DNA replication inhibitors. Nucleic Acids Res. 1993;21: 3997–4004. 8371975

6. Ge XQ, Jackson DA, Blow JJ. Dormant origins licensed by excess Mcm2-7 are required for human cells to survive replicative stress. Genes Dev. 2007;21: 3331–3341. 18079179

7. Ibarra A, Schwob E, Méndez J. Excess MCM proteins protect human cells from replicative stress by licensing backup origins of replication. Proceedings of the National Academy of Sciences. 2008;105: 8956–8961.

8. Alvino GM, Collingwood D, Murphy JM, Delrow J, Brewer BJ, Raghuraman MK. Replication in Hydroxyurea: It's a Matter of Time. Mol Cell Biol. 2007;27: 6396–6406. 17636020

9. Feijoo C, Hall-Jackson C, Wu R, Jenkins D, Leitch J, Gilbert DM, et al. Activation of mammalian Chk1 during DNA replication arrest: a role for Chk1 in the intra-S phase checkpoint monitoring replication origin firing. J Cell Biol. Rockefeller Univ Press; 2001;154: 913–923.

10. Heffernan TP, Simpson DA, Frank AR, Heinloth AN, Paules RS, Cordeiro-Stone M, et al. An ATR- and Chk1-dependent S checkpoint inhibits replicon initiation following UVC-induced DNA damage. Mol Cell Biol. 2002;22: 8552–8561. 12446774

11. Mickle KL, Ramanathan S, Rosebrock A, Oliva A, Chaudari A, Yompakdee C, et al. Checkpoint independence of most DNA replication origins in fission yeast. BMC Mol Biol. BioMed Central Ltd; 2007;8: 112.

12. Adachi S, Minamisawa K, Okushima Y, Inagaki S, Yoshiyama K, Kondou Y, et al. Programmed induction of endoreduplication by DNA double-strand breaks in Arabidopsis. Proceedings of the National Academy of Sciences. National Acad Sciences; 2011;108: 10004–10009.

13. Karrer KM. Nuclear dualism. Methods Cell Biol. 2012;109: 29–52. doi: 10.1016/B978-0-12-385967-9.00003-7 22444142

14. Bodenbender J, Prohaska A, Jauker F, Hipke H, Cleffmann G. DNA elimination and its relation to quantities in the macronucleus of Tetrahymena. Dev Genet. 1992;13: 103–110. 1499151

15. Doerder FP, Ditaranto J, DeBault LE. Evolutionary constraints on quantitative variation and regulation of macronuclear dna content in the genus Tetrahymena. J Cell Sci. 1981;49: 177–193. 7309804

16. Yakisich JS, Sandoval PY, Morrison TL, Kapler GM. TIF1 activates the intra-S-phase checkpoint response in the diploid micronucleus and amitotic polyploid macronucleus of Tetrahymena. Mol Biol Cell. 2006;17: 5185–5197. 17005912

17. Loidl J, Mochizuki K. Tetrahymena meiotic nuclear reorganization is induced by a checkpoint kinase-dependent response to DNA damage. Mol Biol Cell. 2009;20: 2428–2437. doi: 10.1091/mbc.E08-10-1058 19297526

18. Lee P-H, Meng X, Kapler GM. Developmental Regulation of the Tetrahymena thermophila Origin Recognition Complex. PLoS Genet. Public Library of Science; 2015;11: e1004875.

19. Shimada K, Pasero P, Gasser SM. ORC and the intra-S-phase checkpoint: a threshold regulates Rad53p activation in S phase. Genes Dev. 2002;16: 3236–3252. 12502744

20. Takahashi TS, Wigley DB, Walter JC. Pumps, paradoxes and ploughshares: mechanism of the MCM2-7 DNA helicase. Trends Biochem Sci. 2005;30: 437–444. 16002295

21. Meister P, Taddei A, Ponti A, Baldacci G, Gasser SM. Replication foci dynamics: replication patterns are modulated by S-phase checkpoint kinases in fission yeast. The EMBO Journal. 2007;26: 1315–1326. 17304223

22. Smith JJ, Yakisich JS, Kapler GM, Cole ES, Romero DP. A beta-tubulin mutation selectively uncouples nuclear division and cytokinesis in Tetrahymena thermophila. Eukaryotic Cell. 2004;3: 1217–1226. 15470250

23. Morrison TL, Yakisich JS, Cassidy-Hanley D, Kapler GM. TIF1 Represses rDNA replication initiation, but promotes normal S phase progression and chromosome transmission in Tetrahymena. Mol Biol Cell. 2005;16: 2624–2635. 15772155

24. Cleffmann G. Chromatin elimination and the genetic organisation of the macronucleus in Tetrahymena thermophila. Chromosoma. 1980;78: 313–325. 7389513

25. Gao S, Xiong J, Zhang C, Berquist BR, Yang R, Zhao M, et al. Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation. Genes Dev. 2013;27: 1662–1679. doi: 10.1101/gad.218966.113 23884606

26. Talasz H, Helliger W, Sarg B, Debbage PL, Puschendorf B, Lindner H. Hyperphosphorylation of histone H2A.X and dephosphorylation of histone H1 subtypes in the course of apoptosis. Cell Death Differ. 2002;9: 27–39. 11803372

27. Aparicio JG, Viggiani CJ, Gibson DG, Aparicio OM. The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae. Mol Cell Biol. 2004;24: 4769–4780. 15143171

28. Aggarwal BD, Calvi BR. Chromatin regulates origin activity in Drosophila follicle cells. Nature. 2004;430: 372–376. 15254542

29. Mantiero D, Mackenzie A, Donaldson A, Zegerman P. Limiting replication initiation factors execute the temporal programme of origin firing in budding yeast. EMBO J. 2011;30: 4805–4814. doi: 10.1038/emboj.2011.404 22081107

30. Komata M, Bando M, Araki H, Shirahige K. The direct binding of Mrc1, a checkpoint mediator, to Mcm6, a replication helicase, is essential for the replication checkpoint against methyl methanesulfonate-induced stress. Mol Cell Biol. American Society for Microbiology; 2009;29: 5008–5019.

31. MacAlpine DM, Zhang Z, Kapler GM. Type I elements mediate replication fork pausing at conserved upstream sites in the Tetrahymena thermophila ribosomal DNA minichromosome. Mol Cell Biol. 1997;17: 4517–4525. 9234709

32. Mohammad MM, Donti TR, Sebastian Yakisich J, Smith AG, Kapler GM. Tetrahymena ORC contains a ribosomal RNA fragment that participates in rDNA origin recognition. EMBO J. 2007;26: 5048–5060. 18007594

33. Donti TR, Datta S, Sandoval PY, Kapler GM. Differential targeting of Tetrahymena ORC to ribosomal DNA and non-rDNA replication origins. EMBO J. 2009;28: 223–233. doi: 10.1038/emboj.2008.282 19153611

34. Tuduri S, Tourrière H, Pasero P. Defining replication origin efficiency using DNA fiber assays. Chromosome Research. Springer Netherlands; 2010;18: 91–102.

35. Ly T, Ahmad Y, Shlien A, Soroka D, Mills A, Emanuele MJ, et al. A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells. Elife. 2014;3: e01630. doi: 10.7554/eLife.01630 24596151

36. Cleffmann G. Amount of DNA produced during extra S phases in Tetrahymena. J Cell Biol. 1975;66: 204–209. 806601

37. Doerder FP, DeBault LE. Life cycle variation and regulation of macronuclear DNA content in Tetrahymena thermophila. Chromosoma. 1978;69: 1–19. 738160

38. Biradar DP, Rayburn AL. Flow Cytometric Probing of Chromatin Condensation in Maize Diploid Nuclei. New Phytologist. 1994;126: 31–35.

39. Malik P, Zuleger N, las Heras de JI, Saiz-Ros N, Makarov AA, Lazou V, et al. NET23/STING promotes chromatin compaction from the nuclear envelope. PLoS ONE. 2014;9: e111851. doi: 10.1371/journal.pone.0111851 25386906

40. Shechter D, Gautier J. MCM proteins and checkpoint kinases get together at the fork. Proc Natl Acad Sci USA. 2004;101: 10845–10846. 15263078

41. Stead BE, Brandl CJ, Sandre MK, Davey MJ. Mcm2 phosphorylation and the response to replicative stress. BMC Genet. BioMed Central Ltd; 2012;13: 36.

42. Anglana M, Apiou F, Bensimon A, Debatisse M. Dynamics of DNA replication in mammalian somatic cells: nucleotide pool modulates origin choice and interorigin spacing. Cell. 2003;114: 385–394. 12914702

43. Diffley J, Bousset K, Labib K, Noton EA, Santocanale C, Tercero JA. Coping with and recovering from hydroxyurea-induced replication fork arrest in budding yeast. Cold Spring Harb Symp Quant Biol. 2000;65: 333–342. 12760047

44. Alzu A, Bermejo R, Begnis M, Lucca C, Piccini D, Carotenuto W, et al. Senataxin Associates with Replication Forks to Protect Fork Integrity across RNA-Polymerase-II-Transcribed Genes. Cell. Elsevier Inc; 2012;151: 835–846.

45. Claycomb JM, MacAlpine DM, Evans JG, Bell SP, Orr-Weaver TL. Visualization of replication initiation and elongation in Drosophila. J Cell Biol. Rockefeller Univ Press; 2002;159: 225–236.

46. Karnani N, Dutta A. The effect of the intra-S-phase checkpoint on origins of replication in human cells. Genes Dev. 2011;25: 621–633. doi: 10.1101/gad.2029711 21406556

47. Hoggard T, Shor E, Müller CA, Nieduszynski CA, Fox CA. A Link between ORC-Origin Binding Mechanisms and Origin Activation Time Revealed in Budding Yeast. PLoS Genet. 2013;9: e1003798.

48. Jasencakova Z, Scharf AND, Ask K, Corpet A, Imhof A, Almouzni G, et al. Replication stress interferes with histone recycling and predeposition marking of new histones. Mol Cell. 2010;37: 736–743. doi: 10.1016/j.molcel.2010.01.033 20227376

49. Hawkins M, Malla S, Blythe MJ, Nieduszynski CA, Allers T. Accelerated growth in the absence of DNA replication origins. Nature. 2013;503: 544–547. doi: 10.1038/nature12650 24185008

50. Challberg MD, Desiderio SV, Kelly TJ. Adenovirus DNA replication in vitro: characterization of a protein covalently linked to nascent DNA strands. Proc Natl Acad Sci USA. 1980;77: 5105–5109. 6933548

51. Cordell B, Swanstrom R, Goodman HM, Bishop JM. tRNATrp as primer for RNA-directed DNA polymerase: structural determinants of function. J Biol Chem. 1979;254: 1866–1874. 84811

52. Stuckey R, García-Rodríguez N, Aguilera A, Wellinger RE. Role for RNA:DNA hybrids in origin-independent replication priming in a eukaryotic system. Proceedings of the National Academy of Sciences. National Acad Sciences; 2015;: 201501769.

53. Mochizuki K, Gorovsky MA. A Dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase. Genes Dev. 2005;19: 77–89. 15598983

54. Malone CD, Anderson AM, Motl JA, Rexer CH, Chalker DL. Germ line transcripts are processed by a Dicer-like protein that is essential for developmentally programmed genome rearrangements of Tetrahymena thermophila. Mol Cell Biol. 2005;25: 9151–9164. 16199890

55. Lee SR, Collins K. Two classes of endogenous small RNAs in Tetrahymena thermophila. Genes Dev. Cold Spring Harbor Lab; 2006;20: 28–33.

56. Sher N, Bell GW, Li S, Nordman J, Eng T, Eaton ML, et al. Developmental control of gene copy number by repression of replication initiation and fork progression. Genome Res. Cold Spring Harbor Lab; 2012;22: 64–75.

57. Park SY, Asano M. The origin recognition complex is dispensable for endoreplication in Drosophila. Proceedings of the National Academy of Sciences. National Acad Sciences; 2008;105: 12343–12348.

58. Zhang Z, MacAlpine DM, Kapler GM. Developmental regulation of DNA replication: replication fork barriers and programmed gene amplification in Tetrahymena thermophila. Mol Cell Biol. 1997;17: 6147–6156. 9315675

59. Stewart JA, Wang F, Chaiken MF, Kasbek C, Chastain PD, Wright WE, et al. Human CST promotes telomere duplex replication and general replication restart after fork stalling. EMBO J. Nature Publishing Group; 2012;31: 3537–3549.

60. Palen TE, Cech TR. Chromatin structure at the replication origins and transcription-initiation regions of the ribosomal RNA genes of Tetrahymena. Cell. 1984;36: 933–942. 6323028

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