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Characterization of Interaction of the MBP-Tagged MuRif1-C-Terminal Domain with G-Quadruplex DNA by SPR

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Abstract

One of the main players in the cell-specific replication timing pattern is Rap1 interacting factor-1 (Rif1). Rif1 protein consists of N-terminal and C-terminal domains and an intrinsically disordered region in between. It has been suggested that both N- and C-termini of Rif1 are capable of binding to DNA with particularly high affinity to cruciform DNA structures. In the present study, we expressed, solubilized, and purified the maltose-binding protein-tagged murine Rif1 C-terminal domain (MBP-muRif1-CTD). Biological activity of the purified protein was assessed by the electrophoretic mobility shift assay (EMSA) and surface plasmon resonance (SPR). Our results show that the MBP-muRif1-CTD binds G-quadruplex (G4) structure with high affinity (KD 19.0 ± 0.8 nM), as was previously suggested. This study is the first step in investigation of the interaction of MBP-Profinity eXact-muRif1-CTD and G4 by SPR.

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Abbreviations

EMSA:

electrophoretic mobility shift assay

MBP:

maltose binding protein

Rif1:

Rap1-interacting factor 1

SPR:

surface plasmon resonance

References

  1. Rhind, N., and Gilbert, D. M. (2013) DNA replication timing, Cold Spring Harb. Perspect. Biol., 5, a010132, https://doi.org/10.1101/cshperspect.a010132.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Hardy, C. F., Sussel, L., and Shore, D. (1992) A RAP1-interacting protein involved in transcriptional silencing and telomere length regulation, Genes Dev., 6, 801-814.

    Article  CAS  Google Scholar 

  3. Kedziora, S., Gali, V. K., Wilson, R. H. C., Clark, K. R. M., Nieduszynski, C. A., et al. (2018) Rif1 acts through Protein Phosphatase 1 but independent of replication timing to suppress telomere extension in budding yeast, Nucleic Acids Res., 46, 3993-4003, https://doi.org/10.1093/nar/gky132.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Cornacchia, D., Dileep, V., Quivy, J. P., Foti, R., Tili, F., et al. (2012) Mouse Rif1 is a key regulator of the replication-timing programme in mammalian cells, EMBO J., 31, 3678-3690, https://doi.org/10.1038/emboj.2012.214.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Hayano, M., Kanoh, Y., Matsumoto, S., Renard-Guillet, C., Shirahige, K., and Masai, H. (2012) Rif1 is a global regulator of timing of replication origin firing in fission yeast, Genes Dev., 26, 137-150, https://doi.org/10.1101/gad.178491.111.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Yamazaki, S., Ishii, A., Kanoh, Y., Oda, M., Nishito, Y., and Masai, H. (2012) Rif1 regulates the replication timing domains on the human genome, EMBO J., 31, 3667-3677, https://doi.org/10.1038/emboj.2012.180.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Escribano-Diaz, C., Orthwein, A., Fradet-Turcotte, A., Xing, M., Young, J. T., et al. (2013) A cell cycle-dependent regulatory circuit composed of 53BP1-RIF1 and BRCA1-CtIP controls DNA repair pathway choice, Mol. Cell, 49, 872-883, https://doi.org/10.1016/j.molcel.2013.01.001.

    Article  CAS  PubMed  Google Scholar 

  8. Silverman, J., Takai, H., Buonomo, S. B., Eisenhaber, F., and de Lange, T. (2004) Human Rif1, ortholog of a yeast telomeric protein, is regulated by ATM and 53BP1 and functions in the S-phase checkpoint, Genes Dev., 18, 2108-2119, https://doi.org/10.1101/gad.1216004.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Xu, D., Muniandy, P., Leo, E., Yin, J., Thangavel, S., et al. (2010) Rif1 provides a new DNA-binding interface for the Bloom syndrome complex to maintain normal replication, EMBO J., 29, 3140-3155, https://doi.org/10.1038/emboj.2010.186.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Sreesankar, E., Senthilkumar, R., Bharathi, V., Mishra, R. K., and Mishra, K. (2012) Functional diversification of yeast telomere associated protein, Rif1, in higher eukaryotes, BMC Genomics, 13, 255, https://doi.org/10.1186/1471-2164-13-255.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Sukackaite, R., Jensen, M. R., Mas, P. J., Blackledge, M., Buonomo, S. B., and Hart, D. J. (2014) Structural and biophysical characterization of murine rif1 C-terminus reveals high specificity for DNA cruciform structures, J. Biol. Chem., 289, 13903-13911, https://doi.org/10.1074/jbc.M114.557843.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Kanoh, Y., Matsumoto, S., Fukatsu, R., Kakusho, N., Kono, N., et al. (2015) Rif1 binds to G quadruplexes and suppresses replication over long distances, Nat. Struct. Mol. Biol., 22, 889-897, https://doi.org/10.1038/nsmb.3102.

    Article  CAS  PubMed  Google Scholar 

  13. Moriyama, K., Yoshizawa-Sugata, N., and Masai, H. (2018) Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture, J. Biol. Chem., 293, 3607-3624, https://doi.org/10.1074/jbc.RA117.000446.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Kobayashi, S., Fukatsu, R., Kanoh, Y., Kakusho, N., Matsumoto, S., et al. (2019) Both a unique motif at the C-terminus and an N-terminal HEAT repeat contribute to G-quadruplex binding and origin regulation by the Rif1 protein, Mol. Cell. Biol., 39, https://doi.org/10.1128/MCB.00364-18.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Masai, H., Fukatsu, R., Kakusho, N., Kanoh, Y., Moriyama, K., et al. (2019) Rif1 promotes association of G-quadruplex (G4) by its specific G4 binding and oligomerization activities, Sci. Rep., 9, 8618, https://doi.org/10.1038/s41598-019-44736-9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Wang, H., Zhao, A., Chen, L., Zhong, X., Liao, J., et al. (2009) Human RIF1 encodes an anti-apoptotic factor required for DNA repair, Carcinogenesis, 30, 1314-1319, https://doi.org/10.1093/carcin/bgp136.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Mei, Y., Peng, C., Liu, Y. B., Wang, J., and Zhou, H. H. (2017) Silencing RIF1 decreases cell growth, migration and increases cisplatin sensitivity of human cervical cancer cells, Oncotarget, 8, 107044-107051, https://doi.org/10.18632/oncotarget.22315.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Liu, Y. B., Mei, Y., Long, J., Zhang, Y., Hu, D. L., and Zhou, H. H. (2018) RIF1 promotes human epithelial ovarian cancer growth and progression via activating human telomerase reverse transcriptase expression, J. Exp. Clin. Cancer Res., 37, 182, https://doi.org/10.1186/s13046-018-0854-8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Mariani, S., and Minunni, M. (2014) Surface plasmon resonance applications in clinical analysis, Anal. Bioanal. Chem., 406, 2303-2323, https://doi.org/10.1007/s00216-014-7647-5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Nguyen, H. H., Park, J., Kang, S., and Kim, M. (2015) Surface plasmon resonance: a versatile technique for biosensor applications, Sensors (Basel), 15, 10481-10510, https://doi.org/10.3390/s150510481.

    Article  CAS  Google Scholar 

  21. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4, Nature, 227, 680-685.

    Article  CAS  Google Scholar 

  22. Gabelica, V., Maeda, R., Fujimoto, T., Yaku, H., Murashima, T., et al. (2013) Multiple and cooperative binding of fluorescence light-up probe thioflavin T with human telomere DNA G-quadruplex, Biochemistry, 52, 5620-5628, https://doi.org/10.1021/bi4006072.

    Article  CAS  PubMed  Google Scholar 

  23. Renaud de la Faverie, A., Guedin, A., Bedrat, A., Yatsunyk, L. A., and Mergny, J. L. (2014) Thioflavin T as a fluorescence light-up probe for G4 formation, Nucleic Acids Res., 42, e65, https://doi.org/10.1093/nar/gku111.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Carvalho, J., Queiroz, J. A., and Cruz, C. (2017) Circular dichroism of G-quadruplex: a laboratory experiment for the study of topology and ligand binding, J. Chem. Educ., 94, 1547-1551, https://doi.org/10.1021/acs.jchemed.7b00160.

    Article  CAS  Google Scholar 

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Acknowledgments

The authors are grateful to Prof. Masai and Dr. Kenji from the Tokyo Metropolitan Institute of Medical Science, Japan, for sharing their pearls of wisdom during the research and their generous contribution of different muRif1 constructs and their assistance in executing the EMSA assay in this study.

Funding

This work was financially supported by the research core of the Tarbiat Modares University, Iran (grant no. IG-39707).

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Authors and Affiliations

  1. Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran

    Hamed Ghadiri, Bahareh Dabirmanesh & Khosro Khajeh

  2. Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran

    Sana Alavi & Khosro Khajeh

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  1. Hamed Ghadiri
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  2. Sana Alavi
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  3. Bahareh Dabirmanesh
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Correspondence to Khosro Khajeh.

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The authors declare no conflict of interest in financial or any other sphere. This article does not contain descriptions of studies with human participants or animals performed by any of the authors.

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Ghadiri, H., Alavi, S., Dabirmanesh, B. et al. Characterization of Interaction of the MBP-Tagged MuRif1-C-Terminal Domain with G-Quadruplex DNA by SPR. Biochemistry Moscow 86, 898–905 (2021). https://doi.org/10.1134/S0006297921070105

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  • DOI: https://doi.org/10.1134/S0006297921070105

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