Advertisement

Modeling the interplay between DNA-PK, Artemis, and ATM in non-homologous end-joining repair in G1 phase of the cell cycle

  • Maryam RouhaniEmail author
Original Paper

Abstract

Modeling a biological process equips us with more comprehensive insight into the process and a more advantageous experimental design. Non-homologous end joining (NHEJ) is a major double-strand break (DSB) repair pathway that occurs throughout the cell cycle. The objective of the current work is to model the fast and slow phases of NHEJ in G1 phase of the cell cycle following exposure to ionizing radiation (IR). The fast phase contains the major components of NHEJ; Ku70/80 complex, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and XLF/XRCC4/ligase IV complex (XXL). The slow phase in G1 phase of the cell cycle is associated with more complex lesions and involves ATM and Artemis proteins in addition to the major components. Parameters are mainly obtained from experimental data. The model is successful in predicting the kinetics of DSB foci in 13 normal, ATM-deficient, and Artemis-deficient mammalian fibroblast cell lines in G1 phase of the cell cycle after exposure to low doses of IR. The involvement of ATM provides the model with the potency to be connected to different signaling pathways. Ku70/80 concentration and DNA-binding rate as well as XXL concentration and enzymatic activity are introduced as the best targets for affecting NHEJ DSB repair process. On the basis of the current model, decreasing concentration and DNA binding rate of DNA-PKcs is more effective than inhibiting its activity towards the Artemis protein.

Keywords

Mathematical modeling NHEJ repair ATM Artemis DNA-PKcs 

Abbreviations

ATM

Ataxia telangiectasia mutated

CC

Correlation coefficient

DNA-PKcs

DNA-dependent protein kinase catalytic subunit

DSB

Double-strand break

HR

Homologous recombination

IR

Ionizing radiation

Ku

Ku70/80 complex

MEF

Mouse embryonic fibroblast

NHEJ

Non-homologous end joining

PIKK

Phosphatidylinositol 3-kinase-related kinase

XLF

XRCC4-like factor

XXL

XLF/XRCC4/ligase IV complex

Notes

Acknowledgements

The Institute for Advanced Studies in Basic Sciences (IASBS) is acknowledged for supporting this work.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

References

  1. 1.
    Hall, E.J., Giaccia, A.J.: Radiobiology for the Radiologist. Lippincott Williams & Wilkins, Philadelphia (2005)Google Scholar
  2. 2.
    Srivastava, M., Raghavan, S.C.: DNA double-strand break repair inhibitors as cancer therapeutics. Chem. Biol. 22(1), 17–29 (2015)Google Scholar
  3. 3.
    Shrivastav, M., De Haro, L.P., Nickoloff, J.A.: Regulation of DNA double-strand break repair pathway choice. Cell Res. 18(1), 134–147 (2008)Google Scholar
  4. 4.
    Walker, J.R., Corpina, R.A., Goldberg, J.: Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature 412(6847), 607–614 (2001)ADSGoogle Scholar
  5. 5.
    Yoo, S., Dynan, W.S.: Geometry of a complex formed by double strand break repair proteins at a single DNA end: recruitment of DNA-PKcs induces inward translocation of Ku protein. Nucleic Acids Res. 27(24), 4679–4686 (1999)Google Scholar
  6. 6.
    Uematsu, N., Weterings, E., Yano, K., Morotomi-Yano, K., Jakob, B., Taucher-Scholz, G., Mari, P.O., van Gent, D.C., Chen, B.P., Chen, D.J.: Autophosphorylation of DNA-PKCS regulates its dynamics at DNA double-strand breaks. J. Cell Biol. 177(2), 219–229 (2007)Google Scholar
  7. 7.
    Ahnesorg, P., Smith, P., Jackson, S.P.: XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining. Cell 124(2), 301–313 (2006)Google Scholar
  8. 8.
    Grawunder, U., Wilm, M., Wu, X., Kulesza, P., Wilson, T.E., Mann, M., Lieber, M.R.: Activity of DNA ligase IV stimulated by complex formation with XRCC4 protein in mammalian cells. Nature 388(6641), 492–495 (1997)ADSGoogle Scholar
  9. 9.
    Tsai, C.J., Kim, S.A., Chu, G.: Cernunnos/XLF promotes the ligation of mismatched and noncohesive DNA ends. Proc. Natl. Acad. Sci. U. S. A. 104(19), 7851–7856 (2007)ADSGoogle Scholar
  10. 10.
    Riballo, E., Kuhne, M., Rief, N., Doherty, A., Smith, G.C., Recio, M.J., Reis, C., Dahm, K., Fricke, A., Krempler, A., Parker, A.R., Jackson, S.P., Gennery, A., Jeggo, P.A., Lobrich, M.: A pathway of double-strand break rejoining dependent upon ATM, Artemis, and proteins locating to gamma-H2AX foci. Mol. Cell 16(5), 715–724 (2004)Google Scholar
  11. 11.
    Goodarzi, A.A., Noon, A.T., Deckbar, D., Ziv, Y., Shiloh, Y., Lobrich, M., Jeggo, P.A.: ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin. Mol. Cell 31(2), 167–177 (2008)Google Scholar
  12. 12.
    Brandsma, I., Gent, D.C.: Pathway choice in DNA double strand break repair: observations of a balancing act. Genome Integr. 3(1), 9 (2012)Google Scholar
  13. 13.
    Darroudi, F., Wiegant, W., Meijers, M., Friedl, A.A., van der Burg, M., Fomina, J., van Dongen, J.J., van Gent, D.C., Zdzienicka, M.Z.: Role of Artemis in DSB repair and guarding chromosomal stability following exposure to ionizing radiation at different stages of cell cycle. Mutat. Res. 615(1–2), 111–124 (2007)Google Scholar
  14. 14.
    Kuhne, M., Riballo, E., Rief, N., Rothkamm, K., Jeggo, P.A., Lobrich, M.: A double-strand break repair defect in ATM-deficient cells contributes to radiosensitivity. Cancer Res. 64(2), 500–508 (2004)Google Scholar
  15. 15.
    Sokhansanj, B.A., Rodrigue, G.R., Fitch, J.P., Wilson III, D.M.: A quantitative model of human DNA base excision repair. I. Mechanistic insights. Nucleic Acids Res. 30(8), 1817–1825 (2002)Google Scholar
  16. 16.
    Taleei, R., Weinfeld, M., Nikjoo, H.: A kinetic model of single-strand annealing for the repair of DNA double-strand breaks. Radiat. Prot. Dosim. 143(2–4), 191–195 (2011)Google Scholar
  17. 17.
    Politi, A., Mone, M.J., Houtsmuller, A.B., Hoogstraten, D., Vermeulen, W., Heinrich, R., van Driel, R.: Mathematical modeling of nucleotide excision repair reveals efficiency of sequential assembly strategies. Mol. Cell 19(5), 679–690 (2005)Google Scholar
  18. 18.
    Kesseler, K.J., Kaufmann, W.K., Reardon, J.T., Elston, T.C., Sancar, A.: A mathematical model for human nucleotide excision repair: damage recognition by random order assembly and kinetic proofreading. J. Theor. Biol. 249(2), 361–375 (2007)MathSciNetGoogle Scholar
  19. 19.
    Crooke, P.S., Parl, F.F.: A mathematical model for DNA damage and repair. J Nucleic Acids (2010).  https://doi.org/10.4061/2010/352603
  20. 20.
    Rahmanian, S., Taleei, R., Nikjoo, H.: Radiation induced base excision repair (BER): a mechanistic mathematical approach. DNA Repair (Amst.) 22, 89–103 (2014)Google Scholar
  21. 21.
    Nagel, Z.D., Kitange, G.J., Gupta, S.K., Joughin, B.A., Chaim, I.A., Mazzucato, P., Lauffenburger, D.A., Sarkaria, J.N., Samson, L.D.: DNA repair capacity in multiple pathways predicts chemoresistance in glioblastoma multiforme. Cancer Res. 77(1), 198–206 (2017)Google Scholar
  22. 22.
    Friedland, W., Jacob, P., Kundrat, P.: Mechanistic simulation of radiation damage to DNA and its repair: on the track towards systems radiation biology modelling. Radiat. Prot. Dosim. 143(2–4), 542–548 (2011)Google Scholar
  23. 23.
    Friedland, W., Kundrat, P., Jacob, P.: Stochastic modelling of DSB repair after photon and ion irradiation. Int. J. Radiat. Biol. 88(1–2), 129–136 (2012)Google Scholar
  24. 24.
    Cucinotta, F.A., Pluth, J.M., Anderson, J.A., Harper, J.V., O’Neill, P.: Biochemical kinetics model of DSB repair and induction of gamma-H2AX foci by non-homologous end joining. Radiat. Res. 169(2), 214–222 (2008)ADSGoogle Scholar
  25. 25.
    Li, Y., Cucinotta, F.A.: Modeling non-homologous end joining. J. Theor. Biol. 283(1), 122–135 (2011)MathSciNetzbMATHGoogle Scholar
  26. 26.
    Taleei, R., Nikjoo, H.: Repair of the double-strand breaks induced by low energy electrons: a modelling approach. Int. J. Radiat. Biol. 88(12), 948–953 (2012)Google Scholar
  27. 27.
    Taleei, R., Nikjoo, H.: The non-homologous end-joining (NHEJ) pathway for the repair of DNA double-strand breaks: I. A mathematical model. Radiat. Res. 179(5), 530–539 (2013)ADSGoogle Scholar
  28. 28.
    Taleei, R., Girard, P.M., Sankaranarayanan, K., Nikjoo, H.: The non-homologous end-joining (NHEJ) mathematical model for the repair of double-strand breaks: II. Application to damage induced by ultrasoft X-rays and low-energy electrons. Radiat. Res. 179(5), 540–548 (2013)ADSGoogle Scholar
  29. 29.
    Dolan, D., Nelson, G., Zupanic, A., Smith, G., Shanley, D.: Systems modelling of NHEJ reveals the importance of redox regulation of Ku70/80 in the dynamics of DNA damage foci. PLoS One 8(2), e55190 (2013)ADSGoogle Scholar
  30. 30.
    Taleei, R., Nikjoo, H.: Biochemical DSB-repair model for mammalian cells in G1 and early S phases of the cell cycle. Mutat. Res. 756(1–2), 206–212 (2013)Google Scholar
  31. 31.
    Li, Y., Reynolds, P., O’Neill, P., Cucinotta, F.A.: Modeling damage complexity-dependent non-homologous end-joining repair pathway. PLoS One 9(2), e85816 (2014)ADSGoogle Scholar
  32. 32.
    Belov, O.V., Krasavin, E.A., Lyashko, M.S., Batmunkh, M., Sweilam, N.H.: A quantitative model of the major pathways for radiation-induced DNA double-strand break repair. J. Theor. Biol. 366, 115–130 (2015)MathSciNetGoogle Scholar
  33. 33.
    Mohapatra, S., Kawahara, M., Khan, I.S., Yannone, S.M., Povirk, L.F.: Restoration of G1 chemo/radioresistance and double-strand-break repair proficiency by wild-type but not endonuclease-deficient Artemis. Nucleic Acids Res. 39(15), 6500–6510 (2011)Google Scholar
  34. 34.
    Rothkamm, K., Lobrich, M.: Evidence for a lack of DNA double-strand break repair in human cells exposed to very low x-ray doses. Proc. Natl. Acad. Sci. U. S. A. 100(9), 5057–5062 (2003)ADSGoogle Scholar
  35. 35.
    Sun, J., Lee, K.J., Davis, A.J., Chen, D.J.: Human Ku70/80 protein blocks exonuclease 1-mediated DNA resection in the presence of human Mre11 or Mre11/Rad50 protein complex. J. Biol. Chem. 287(7), 4936–4945 (2012)Google Scholar
  36. 36.
    Chan, D.W., Chen, B.P., Prithivirajsingh, S., Kurimasa, A., Story, M.D., Qin, J., Chen, D.J.: Autophosphorylation of the DNA-dependent protein kinase catalytic subunit is required for rejoining of DNA double-strand breaks. Genes Dev. 16(18), 2333–2338 (2002)Google Scholar
  37. 37.
    West, R.B., Yaneva, M., Lieber, M.R.: Productive and nonproductive complexes of Ku and DNA-dependent protein kinase at DNA termini. Mol. Cell. Biol. 18(10), 5908–5920 (1998)Google Scholar
  38. 38.
    Mari, P.O., Florea, B.I., Persengiev, S.P., Verkaik, N.S., Bruggenwirth, H.T., Modesti, M., Giglia-Mari, G., Bezstarosti, K., Demmers, J.A., Luider, T.M., Houtsmuller, A.B., van Gent, D.C.: Dynamic assembly of end-joining complexes requires interaction between Ku70/80 and XRCC4. Proc. Natl. Acad. Sci. U. S. A. 103(49), 18597–18602 (2006)ADSGoogle Scholar
  39. 39.
    Nick McElhinny, S.A., Snowden, C.M., McCarville, J., Ramsden, D.A.: Ku recruits the XRCC4-ligase IV complex to DNA ends. Mol. Cell. Biol. 20(9), 2996–3003 (2000)Google Scholar
  40. 40.
    Yano, K., Morotomi-Yano, K., Wang, S.Y., Uematsu, N., Lee, K.J., Asaithamby, A., Weterings, E., Chen, D.J.: Ku recruits XLF to DNA double-strand breaks. EMBO Rep. 9(1), 91–96 (2008)Google Scholar
  41. 41.
    Reynolds, P., Anderson, J.A., Harper, J.V., Hill, M.A., Botchway, S.W., Parker, A.W., O’Neill, P.: The dynamics of Ku70/80 and DNA-PKcs at DSBs induced by ionizing radiation is dependent on the complexity of damage. Nucleic Acids Res. 40(21), 10821–10831 (2012)Google Scholar
  42. 42.
    Hsu, H.L., Yannone, S.M., Chen, D.J.: Defining interactions between DNA-PK and ligase IV/XRCC4. DNA Repair (Amst) 1(3), 225–235 (2002)Google Scholar
  43. 43.
    Calsou, P., Delteil, C., Frit, P., Drouet, J., Salles, B.: Coordinated assembly of Ku and p460 subunits of the DNA-dependent protein kinase on DNA ends is necessary for XRCC4-ligase IV recruitment. J. Mol. Biol. 326(1), 93–103 (2003)Google Scholar
  44. 44.
    Ma, Y., Pannicke, U., Schwarz, K., Lieber, M.R.: Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell 108(6), 781–794 (2002)Google Scholar
  45. 45.
    Wang, J., Pluth, J.M., Cooper, P.K., Cowan, M.J., Chen, D.J., Yannone, S.M.: Artemis deficiency confers a DNA double-strand break repair defect and Artemis phosphorylation status is altered by DNA damage and cell cycle progression. DNA Repair (Amst) 4(5), 556–570 (2005)Google Scholar
  46. 46.
    Ma, Y., Pannicke, U., Lu, H., Niewolik, D., Schwarz, K., Lieber, M.R.: The DNA-dependent protein kinase catalytic subunit phosphorylation sites in human Artemis. J. Biol. Chem. 280(40), 33839–33846 (2005)Google Scholar
  47. 47.
    Zhang, X., Succi, J., Feng, Z., Prithivirajsingh, S., Story, M.D., Legerski, R.J.: Artemis is a phosphorylation target of ATM and ATR and is involved in the G2/M DNA damage checkpoint response. Mol. Cell. Biol. 24(20), 9207–9220 (2004)Google Scholar
  48. 48.
    Niewolik, D., Pannicke, U., Lu, H., Ma, Y., Wang, L.C., Kulesza, P., Zandi, E., Lieber, M.R., Schwarz, K.: DNA-PKcs dependence of Artemis endonucleolytic activity, differences between hairpins and 5′ or 3′ overhangs. J. Biol. Chem. 281(45), 33900–33909 (2006)Google Scholar
  49. 49.
    Lee, J.H., Paull, T.T.: ATM activation by DNA double-strand breaks through the Mre11-Rad50-Nbs1 complex. Science 308(5721), 551–554 (2005)ADSGoogle Scholar
  50. 50.
    Gottlieb, T.M., Jackson, S.P.: The DNA-dependent protein kinase: requirement for DNA ends and association with Ku antigen. Cell 72(1), 131–142 (1993)Google Scholar
  51. 51.
    Lobrich, M., Jeggo, P.A.: Harmonising the response to DSBs: a new string in the ATM bow. DNA Repair (Amst) 4(7), 749–759 (2005)Google Scholar
  52. 52.
    Milo, R., Jorgensen, P., Moran, U., Weber, G., Springer, M.: BioNumbers—the database of key numbers in molecular and cell biology. Nucleic Acids Res. 38(Database issue), D750–D753 (2010)Google Scholar
  53. 53.
    Chang, A., Schomburg, I., Placzek, S., Jeske, L., Ulbrich, M., Xiao, M., Sensen, C.W., Schomburg, D.: BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Res. 43(Database issue), D439–D446 (2015)Google Scholar
  54. 54.
    Chen, L., Trujillo, K., Sung, P., Tomkinson, A.E.: Interactions of the DNA ligase IV-XRCC4 complex with DNA ends and the DNA-dependent protein kinase. J. Biol. Chem. 275(34), 26196–26205 (2000)Google Scholar
  55. 55.
    Teraoka, H., Sawai, M., Tsukada, K.: DNA ligase from mouse Ehrlich ascites tumor cells. J. Biochem. 95(5), 1529–1532 (1984)Google Scholar
  56. 56.
    Anderson, C.W., Carter, T.H.: The DNA-activated protein kinase—DNA-PK. Curr. Top. Microbiol. Immunol. 217, 91–111 (1996)Google Scholar
  57. 57.
    Bakkenist, C.J., Kastan, M.B.: DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature 421(6922), 499–506 (2003)ADSGoogle Scholar
  58. 58.
    Moshous, D., Callebaut, I., de Chasseval, R., Corneo, B., Cavazzana-Calvo, M., Le Deist, F., Tezcan, I., Sanal, O., Bertrand, Y., Philippe, N., Fischer, A., de Villartay, J.P.: Artemis, a novel DNA double-strand break repair/V(D)J recombination protein, is mutated in human severe combined immune deficiency. Cell 105(2), 177–186 (2001)Google Scholar
  59. 59.
    Mimori, T., Hardin, J.A., Steitz, J.A.: Characterization of the DNA-binding protein antigen Ku recognized by autoantibodies from patients with rheumatic disorders. J. Biol. Chem. 261(5), 2274–2278 (1986)Google Scholar
  60. 60.
    Windhofer, F., Wu, W., Iliakis, G.: Low levels of DNA ligases III and IV sufficient for effective NHEJ. J. Cell. Physiol. 213(2), 475–483 (2007)Google Scholar
  61. 61.
    Butch, A.W., Chun, H.H., Nahas, S.A., Gatti, R.A.: Immunoassay to measure ataxia-telangiectasia mutated protein in cellular lysates. Clin. Chem. 50(12), 2302–2308 (2004)Google Scholar
  62. 62.
    Rogakou, E.P., Boon, C., Redon, C., Bonner, W.M.: Megabase chromatin domains involved in DNA double-strand breaks in vivo. J. Cell Biol. 146(5), 905–916 (1999)Google Scholar
  63. 63.
    Ingalls, B.P., Sauro, H.M.: Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. J. Theor. Biol. 222(1), 23–36 (2003)MathSciNetGoogle Scholar
  64. 64.
    Gately, D.P., Hittle, J.C., Chan, G.K., Yen, T.J.: Characterization of ATM expression, localization, and associated DNA-dependent protein kinase activity. Mol. Biol. Cell 9(9), 2361–2374 (1998)Google Scholar
  65. 65.
    Jongmans, W., Vuillaume, M., Chrzanowska, K., Smeets, D., Sperling, K., Hall, J.: Nijmegen breakage syndrome cells fail to induce the p53-mediated DNA damage response following exposure to ionizing radiation. Mol. Cell. Biol. 17(9), 5016–5022 (1997)Google Scholar
  66. 66.
    Shiloh, Y.: ATM and related protein kinases: safeguarding genome integrity. Nat. Rev. Cancer 3(3), 155–168 (2003)Google Scholar
  67. 67.
    Klokov, D., MacPhail, S.M., Banath, J.P., Byrne, J.P., Olive, P.L.: Phosphorylated histone H2AX in relation to cell survival in tumor cells and xenografts exposed to single and fractionated doses of X-rays. Radiother. Oncol. 80(2), 223–229 (2006)Google Scholar
  68. 68.
    Ferguson, D.O., Sekiguchi, J.M., Chang, S., Frank, K.M., Gao, Y., DePinho, R.A., Alt, F.W.: The nonhomologous end-joining pathway of DNA repair is required for genomic stability and the suppression of translocations. Proc. Natl. Acad. Sci. U. S. A. 97(12), 6630–6633 (2000)ADSGoogle Scholar
  69. 69.
    Kasten, U., Plottner, N., Johansen, J., Overgaard, J., Dikomey, E.: Ku70/80 gene expression and DNA-dependent protein kinase (DNA-PK) activity do not correlate with double-strand break (DSB) repair capacity and cellular radiosensitivity in normal human fibroblasts. Br. J. Cancer 79(7–8), 1037–1041 (1999)Google Scholar
  70. 70.
    Poinsignon, C., de Chasseval, R., Soubeyrand, S., Moshous, D., Fischer, A., Hache, R.J., de Villartay, J.P.: Phosphorylation of Artemis following irradiation-induced DNA damage. Eur. J. Immunol. 34(11), 3146–3155 (2004)Google Scholar
  71. 71.
    Goodarzi, A.A., Yu, Y., Riballo, E., Douglas, P., Walker, S.A., Ye, R., Harer, C., Marchetti, C., Morrice, N., Jeggo, P.A., Lees-Miller, S.P.: DNA-PK autophosphorylation facilitates Artemis endonuclease activity. EMBO J. 25(16), 3880–3889 (2006)Google Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of Biological SciencesInstitute for Advanced Studies in Basic Sciences (IASBS)ZanjanIran

Personalised recommendations