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.
Similar content being viewed by others
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
References
Hall, E.J., Giaccia, A.J.: Radiobiology for the Radiologist. Lippincott Williams & Wilkins, Philadelphia (2005)
Srivastava, M., Raghavan, S.C.: DNA double-strand break repair inhibitors as cancer therapeutics. Chem. Biol. 22(1), 17–29 (2015)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Brandsma, I., Gent, D.C.: Pathway choice in DNA double strand break repair: observations of a balancing act. Genome Integr. 3(1), 9 (2012)
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)
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)
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)
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)
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)
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)
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
Rahmanian, S., Taleei, R., Nikjoo, H.: Radiation induced base excision repair (BER): a mechanistic mathematical approach. DNA Repair (Amst.) 22, 89–103 (2014)
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)
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)
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)
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)
Li, Y., Cucinotta, F.A.: Modeling non-homologous end joining. J. Theor. Biol. 283(1), 122–135 (2011)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Teraoka, H., Sawai, M., Tsukada, K.: DNA ligase from mouse Ehrlich ascites tumor cells. J. Biochem. 95(5), 1529–1532 (1984)
Anderson, C.W., Carter, T.H.: The DNA-activated protein kinase—DNA-PK. Curr. Top. Microbiol. Immunol. 217, 91–111 (1996)
Bakkenist, C.J., Kastan, M.B.: DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature 421(6922), 499–506 (2003)
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)
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)
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)
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)
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)
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)
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)
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)
Shiloh, Y.: ATM and related protein kinases: safeguarding genome integrity. Nat. Rev. Cancer 3(3), 155–168 (2003)
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)
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)
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)
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)
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)
Acknowledgements
The Institute for Advanced Studies in Basic Sciences (IASBS) is acknowledged for supporting this work.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflicts of interest.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Rouhani, M. Modeling the interplay between DNA-PK, Artemis, and ATM in non-homologous end-joining repair in G1 phase of the cell cycle. J Biol Phys 45, 127–146 (2019). https://doi.org/10.1007/s10867-018-9519-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10867-018-9519-2