The kinetics of uracil-N-glycosylase distribution inside replication foci
Jazyk angličtina Země Anglie, Velká Británie Médium electronic
Typ dokumentu časopisecké články, práce podpořená grantem
Grantová podpora
NU22-08-00148
Ministerstvo Zdravotnictví Ceské Republiky
TN01000013
Technologická Agentura České Republiky
EXCELES, grant number LX22NPO5102
Ministerstvo Školství, Mládeže a Tělovýchovy
PubMed
39849039
PubMed Central
PMC11757751
DOI
10.1038/s41598-024-84408-x
PII: 10.1038/s41598-024-84408-x
Knihovny.cz E-zdroje
- MeSH
- buněčný cyklus MeSH
- kinetika MeSH
- lidé MeSH
- oprava DNA MeSH
- replikace DNA * MeSH
- S fáze MeSH
- uracil-DNA-glykosidasa * metabolismus MeSH
- uracil metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- uracil-DNA-glykosidasa * MeSH
- uracil MeSH
Mismatched nucleobase uracil is commonly repaired through the base excision repair initiated by DNA uracil glycosylases. The data presented in this study strongly indicate that the nuclear uracil-N-glycosylase activity and nuclear protein content in human cell lines is highest in the S phase of the cell cycle and that its distribution kinetics partially reflect the DNA replication activity in replication foci. In this respect, the data demonstrate structural changes of the replication focus related to the uracil-N-glycosylase distribution several dozens of minutes before end of its replication. The analysis also showed that very popular synchronisation protocols based on the double thymidine block can result in changes in the UNG2 content and uracil excision rate. In response, we propose a new method for the description of the changes of the content and the activity of different cell components during cell cycle without the necessity to use synchronisation protocols.
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Pan, M. R., Li, K., Lin, S. Y. & Hung, W. C. Connecting the dots: From DNA damage and repair to aging. Int. J. Mol. Sci.17, 685. 10.3390/ijms17050685 (2016). PubMed PMC
Mjelle, R. et al. Cell cycle regulation of human DNA repair and chromatin remodeling genes. DNA Repair (Amst)30, 53–67. 10.1016/j.dnarep.2015.03.007 (2015). PubMed
Krokan, H. E. & Bjoras, M. Base excision repair. Cold Spring Harb. Perspect. Biol.5, a012583. 10.1101/cshperspect.a012583 (2013). PubMed PMC
Ligasova, A., Rosenberg, I., Bockova, M., Homola, J. & Koberna, K. Anchored linear oligonucleotides: The effective tool for the real-time measurement of uracil DNA glycosylase activity. Open Biol.11, 210136. 10.1098/rsob.210136 (2021). PubMed PMC
Kavli, B. et al. hUNG2 is the major repair enzyme for removal of uracil from U: A matches, U: G mismatches, and U in single-stranded DNA, with hSMUG1 as a broad specificity backup. J. Biol. Chem.277, 39926–39936. 10.1074/jbc.M207107200 (2002). PubMed
Hardeland, U., Kunz, C., Focke, F., Szadkowski, M. & Schar, P. Cell cycle regulation as a mechanism for functional separation of the apparently redundant uracil DNA glycosylases TDG and UNG2. Nucleic Acids Res.35, 3859–3867. 10.1093/nar/gkm337 (2007). PubMed PMC
Visnes, T., Akbari, M., Hagen, L., Slupphaug, G. & Krokan, H. E. The rate of base excision repair of uracil is controlled by the initiating glycosylase. DNA Repair (Amst.)7, 1869–1881. 10.1016/j.dnarep.2008.07.012 (2008). PubMed
Hardeland, U. et al. Thymine DNA glycosylase. Prog. Nucleic Acid Res. Mol. Biol.68, 235–253. 10.1016/s0079-6603(01)68103-0 (2001). PubMed
Hagen, L. et al. Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA. EMBO J.27, 51–61. 10.1038/sj.emboj.7601958 (2008). PubMed PMC
Haug, T. et al. Regulation of expression of nuclear and mitochondrial forms of human uracil-DNA glycosylase. Nucleic Acids Res.26, 1449–1457. 10.1093/nar/26.6.1449 (1998). PubMed PMC
Fischer, J. A. & Caradonna, S. J. Analysis of nuclear uracil DNA-glycosylase (nUDG) turnover during the cell cycle. Methods Mol. Biol.1524, 177–188. 10.1007/978-1-4939-6603-5_11 (2017). PubMed
Fischer, J. A., Muller-Weeks, S. & Caradonna, S. Proteolytic degradation of the nuclear isoform of uracil-DNA glycosylase occurs during the S phase of the cell cycle. DNA Repair (Amst)3, 505–513. 10.1016/j.dnarep.2004.01.012 (2004). PubMed
Otterlei, M. et al. Post-replicative base excision repair in replication foci. EMBO J.18, 3834–3844. 10.1093/emboj/18.13.3834 (1999). PubMed PMC
Koberna, K. et al. Electron microscopy of DNA replication in 3-D: Evidence for similar-sized replication foci throughout S-phase. J. Cell Biochem.94, 126–138. 10.1002/jcb.20300 (2005). PubMed
Ligasova, A. & Koberna, K. The organisation of replisomes. DNA Replication—Current Advances, 253–268, Book_10.5772/791 (2011).
Ligasova, A., Raska, I. & Koberna, K. Organization of human replicon: Singles or zipping couples?. J. Struct. Biol.165, 204–213. 10.1016/j.jsb.2008.11.004 (2009). PubMed PMC
Sarno, A. et al. Uracil-DNA glycosylase UNG1 isoform variant supports class switch recombination and repairs nuclear genomic uracil. Nucleic Acids Res.47, 4569–4585. 10.1093/nar/gkz145 (2019). PubMed PMC
Hayran, A. B. et al. RPA guides UNG to uracil in ssDNA to facilitate antibody class switching and repair of mutagenic uracil at the replication fork. Nucleic Acids Res.52, 784–800. 10.1093/nar/gkad1115 (2024). PubMed PMC
Micozzi, D. et al. Human cytidine deaminase: A biochemical characterization of its naturally occurring variants. Int. J. Biol. Macromol.63, 64–74. 10.1016/j.ijbiomac.2013.10.029 (2014). PubMed PMC
Vassilev, L. T. Cell cycle synchronization at the G2/M phase border by reversible inhibition of CDK1. Cell Cycle5, 2555–2556. 10.4161/cc.5.22.3463 (2006). PubMed
Vassilev, L. T. et al. Selective small-molecule inhibitor reveals critical mitotic functions of human CDK1. Proc. Natl. Acad. Sci. U. S. A.103, 10660–10665. 10.1073/pnas.0600447103 (2006). PubMed PMC
Ligasova, A. & Koberna, K. Strengths and weaknesses of cell synchronization protocols based on inhibition of DNA synthesis. Int. J. Mol. Sci.10.3390/ijms221910759 (2021). PubMed PMC
Sakaue-Sawano, A. et al. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell132, 487–498. 10.1016/j.cell.2007.12.033 (2008). PubMed
Kaida, A. & Miura, M. Differential dependence on oxygen tension during the maturation process between monomeric Kusabira Orange 2 and monomeric Azami Green expressed in HeLa cells. Biochem. Biophys. Res. Commun.421, 855–859. 10.1016/j.bbrc.2012.04.102 (2012). PubMed
McGarry, T. J. & Kirschner, M. W. Geminin, an inhibitor of DNA replication, is degraded during mitosis. Cell93, 1043–1053. 10.1016/S0092-8674(00)81209-X (1998). PubMed
Nishitani, H., Lygerou, Z. & Nishimoto, T. Proteolysis of DNA replication licensing factor Cdt1 in S-phase is performed independently of Geminin through its N-terminal region. J. Biol. Chem.279, 30807–30816. 10.1074/jbc.M312644200 (2004). PubMed
Yoshida, K. & Inoue, I. Regulation of Geminin and Cdt1 expression by E2F transcription factors. Oncogene23, 3802–3812. 10.1038/sj.onc.1207488 (2004). PubMed
Zielke, N. & Edgar, B. A. FUCCI sensors: Powerful new tools for analysis of cell proliferation. Wiley Interdiscip. Rev. Dev. Biol.4, 469–487. 10.1002/wdev.189 (2015). PubMed PMC
Seluanov, A. et al. Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat. Proc. Natl. Acad. Sci. U. S. A.106, 19352–19357. 10.1073/pnas.0905252106 (2009). PubMed PMC
Petrova, N. V., Velichko, A. K., Razin, S. V. & Kantidze, O. L. Small molecule compounds that induce cellular senescence. Aging Cell15, 999–1017. 10.1111/acel.12518 (2016). PubMed PMC
Gonzalez-Gualda, E., Baker, A. G., Fruk, L. & Munoz-Espin, D. A guide to assessing cellular senescence in vitro and in vivo. FEBS J.288, 56–80. 10.1111/febs.15570 (2021). PubMed
Kudlova, N., De Sanctis, J. B. & Hajduch, M. Cellular senescence: Molecular targets, biomarkers, and senolytic drugs. Int. J. Mol. Sci.10.3390/ijms23084168 (2022). PubMed PMC
Torseth, K. et al. The UNG2 Arg88Cys variant abrogates RPA-mediated recruitment of UNG2 to single-stranded DNA. DNA Repair11, 559–569. 10.1016/j.dnarep.2012.03.006 (2012). PubMed
Zeman, M. K. & Cimprich, K. A. Causes and consequences of replication stress. Nat. Cell Biol.16, 2–9. 10.1038/ncb2897 (2014). PubMed PMC
Darzynkiewicz, Z., Halicka, H. D., Zhao, H. & Podhorecka, M. Cell synchronization by inhibitors of DNA replication induces replication stress and DNA damage response: Analysis by flow cytometry. Methods Mol. Biol.761, 85–96. 10.1007/978-1-61779-182-6_6 (2011). PubMed PMC
Halicka, D. et al. DNA damage response resulting from replication stress induced by synchronization of cells by inhibitors of DNA replication: Analysis by flow cytometry. Methods Mol. Biol.1524, 107–119. 10.1007/978-1-4939-6603-5_7 (2017). PubMed
Kurose, A., Tanaka, T., Huang, X., Traganos, F. & Darzynkiewicz, Z. Synchronization in the cell cycle by inhibitors of DNA replication induces histone H2AX phosphorylation: An indication of DNA damage. Cell Prolif.39, 231–240. 10.1111/j.1365-2184.2006.00380.x (2006). PubMed PMC
Hammond, E. M., Green, S. L. & Giaccia, A. J. Comparison of hypoxia-induced replication arrest with hydroxyurea and aphidicolin-induced arrest. Mutat. Res.532, 205–213. 10.1016/j.mrfmmm.2003.08.017 (2003). PubMed
Gong, J., Traganos, F. & Darzynkiewicz, Z. Growth imbalance and altered expression of cyclins B1, A, E, and D3 in MOLT-4 cells synchronized in the cell cycle by inhibitors of DNA replication. Cell Growth Differ.6, 1485–1493 (1995). PubMed
De Brabander, M. J., Van de Veire, R. M., Aerts, F. E., Borgers, M. & Janssen, P. A. The effects of methyl (5-(2-thienylcarbonyl)-1H-benzimidazol-2-yl) carbamate, (R 17934; NSC 238159), a new synthetic antitumoral drug interfering with microtubules, on mammalian cells cultured in vitro. Cancer Res.36, 905–916 (1976). PubMed
Salmon, E. D., McKeel, M. & Hays, T. Rapid rate of tubulin dissociation from microtubules in the mitotic spindle in vivo measured by blocking polymerization with colchicine. J. Cell Biol.99, 1066–1075. 10.1083/jcb.99.3.1066 (1984). PubMed PMC
Javanmoghadam-Kamrani, S. & Keyomarsi, K. Synchronization of the cell cycle using lovastatin. Cell Cycle7, 2434–2440. 10.4161/cc.6364 (2008). PubMed
Park, S. Y. et al. Mimosine arrests the cell cycle prior to the onset of DNA replication by preventing the binding of human Ctf4/And-1 to chromatin via Hif-1alpha activation in HeLa cells. Cell Cycle11, 761–766. 10.4161/cc.11.4.19209 (2012). PubMed
Zwanenburg, T. S. Standardized shake-off to synchronize cultured CHO cells. Mutat Res.120, 151–159. 10.1016/0165-7992(83)90157-4 (1983). PubMed
Nakamura, H., Morita, T. & Sato, C. Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus. Exp. Cell Res.165, 291–297. 10.1016/0014-4827(86)90583-5 (1986). PubMed
Manders, E. M., Stap, J., Brakenhoff, G. J., van Driel, R. & Aten, J. A. Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy. J. Cell Sci.103(Pt 3), 857–862. 10.1242/jcs.103.3.857 (1992). PubMed
Leonhardt, H. et al. Dynamics of DNA replication factories in living cells. J. Cell Biol.149, 271–280. 10.1083/jcb.149.2.271 (2000). PubMed PMC
Ligasova, A. et al. Dr Jekyll and Mr Hyde: a strange case of 5-ethynyl-2 ’-deoxyuridine and 5-ethynyl-2 ’- deoxycytidine. Open Biol.6, 150172. 10.1098/rsob.150172 (2016). PubMed PMC
Ligasova, A. & Koberna, K. Quantification of fixed adherent cells using a strong enhancer of the fluorescence of DNA dyes. Sci. Rep.9, 8701. 10.1038/s41598-019-45217-9 (2019). PubMed PMC
Ligasova, A., Liboska, R., Rosenberg, I. & Koberna, K. The fingerprint of anti-bromodeoxyuridine antibodies and its use for the assessment of their affinity to 5-bromo-2’-deoxyuridine in cellular DNA under various conditions. PLoS One10, e0132393. 10.1371/journal.pone.0132393 (2015). PubMed PMC
Ligasova, A., Strunin, D., Friedecky, D., Adam, T. & Koberna, K. A fatal combination: A thymidylate synthase inhibitor with DNA damaging activity. PLoS One10, e0117459. 10.1371/journal.pone.0117459 (2015). PubMed PMC
Ligasova, A., Konecny, P., Frydrych, I. & Koberna, K. Cell cycle profiling by image and flow cytometry: The optimised protocol for the detection of replicational activity using 5-Bromo-2’-deoxyuridine, low concentration of hydrochloric acid and exonuclease III. PLoS One12, e0175880. 10.1371/journal.pone.0175880 (2017). PubMed PMC
Ligasova, A., Konecny, P., Frydrych, I. & Koberna, K. Looking for ugly ducklings: The role of the stability of BrdU-antibody complex and the improved method of the detection of DNA replication. PLoS One12, e0174893. 10.1371/journal.pone.0174893 (2017). PubMed PMC
Cvackova, Z. et al. Pontin is localized in nucleolar fibrillar centers. Chromosoma117, 487–497. 10.1007/s00412-008-0170-8 (2008). PubMed PMC
Ligasova, A. et al. A new sensitive method for the detection of mycoplasmas using fluorescence microscopy. Cells8, 1510. 10.3390/cells8121510 (2019). PubMed PMC
Ligasova, A., Pisklakova, B., Friedecky, D. & Koberna, K. A new technique for the analysis of metabolic pathways of cytidine analogues and cytidine deaminase activities in cells. Sci. Rep.13, 20530. 10.1038/s41598-023-47792-4 (2023). PubMed PMC
Romero-Calvo, I. et al. Reversible Ponceau staining as a loading control alternative to actin in Western blots. Anal. Biochem.401, 318–320. 10.1016/j.ab.2010.02.036 (2010). PubMed
Miller, L. P. ImageJ gel analysis, http://www.lukemiller.org/ImageJ_gel_analysis.pdf (2010).
Ligasova, A. & Koberna, K. New Concept and Apparatus for Cytocentrifugation and Cell Processing for Microscopy Analysis. Int J Mol Sci22, 10.3390/ijms22137098 (2021). PubMed PMC
Berg, S. et al. ilastik: Interactive machine learning for (bio)image analysis. Nat. Methods16, 1226–1232. 10.1038/s41592-019-0582-9 (2019). PubMed
Carpenter, A. E. et al. Cell Profiler: Image analysis software for identifying and quantifying cell phenotypes. Genome Biol.7, R100. 10.1186/gb-2006-7-10-r100 (2006). PubMed PMC
Kamentsky, L. et al. Improved structure, function and compatibility for cell profiler: Modular high-throughput image analysis software. Bioinformatics27, 1179–1180. 10.1093/bioinformatics/btr095 (2011). PubMed PMC
Schindelin, J. et al. Fiji: An open-source platform for biological-image analysis. Nat. Methods9, 676–682. 10.1038/nmeth.2019 (2012). PubMed PMC
Van Rossum, G. & Drake, F. L. Python 3 Reference Manual. (Createspace, 2009).
Harris, C. R. et al. Array programming with NumPy. Nature585, 357–362. 10.1038/s41586-020-2649-2 (2020). PubMed PMC
McKinney, W. In Proceedings of the 9th Python in Science Conference 51–56.
Virtanen, P. et al. SciPy 1.0: Fundamental algorithms for scientific computing in Python. Nat. Methods17, 261–272. 10.1038/s41592-019-0686-2 (2020). PubMed PMC
A Rapid Approach for Identifying Cell Lines Lacking Functional Cytidine Deaminase