Advertisement

Exploring the Interaction of Human Ribosomal Protein uS3 with Single-Stranded DNAs Having Different Sequences

  • 11 Accesses

Abstract

The analysis of data on genomic DNA sequences in the binding sites of human ribosomal protein uS3 in vivo, obtained earlier by ChIP-Seq method, was carried out; the presence of significant content of TGGAA repeats, belonging to the type III of human satellites, was found. The dependence of the affinity of the corresponding recombinant protein uS3 to single-stranded DNA and its AP lyase activity on the DNA sequence in vitro, in particular on the presence of TGGAA pentamer repeats, was investigated. It was shown that the presence of these repeats in the model DNAs did not provide an increased affinity to the isolated ribosomal protein uS3. The presence of TCC and TTC motifs in DNA complementary to the corresponding pentamer triplets only slightly increased the affinity of DNA to this protein. It was established that the AP lyase activity of the uS3 protein was also not increased when DNA containing abasic (AP) site contained TGGAA repeats and was independent on the position of the AP site in it. It was shown that the efficiency of single-stranded DNA cleavage at the AP site as a whole correlated with the affinity of uS3 protein to this DNA. It was concluded that the high content of the above repeats in the ribosomal protein uS3 binding sites on chromatin relate to high content of (TGGAA)n repeats in single-stranded DNA regions physically accessible for the protein binding but not to its higher affinity to the pentamer or DNA motifs complementary to it.

This is a preview of subscription content, log in to check access.

Access options

Buy single article

Instant unlimited access to the full article PDF.

US$ 39.95

Price includes VAT for USA

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.

REFERENCES

  1. 1

    Warner, J.R. and McIntosh, K.B., Mol. Cell, 2009, vol. 34, pp. 3–11.

  2. 2

    Hui, L., Yi-fei, Z., Juan, X., Rong, W., and Zhengping, J., Microbiol. Res., 2015, vol. 177, pp. 28–33.

  3. 3

    Franklin, D.A. and Zhang, Y., EncyclopediaCell Biol., 2016, vol. 3, pp. 281–287.

  4. 4

    Graifer, D., Malygin, A., Zharkov, D.O., and Karpova, G., Biochimie, 2014, vol. 99, pp. 8–18.

  5. 5

    Yacoub, A., Augeri, L., Kelley, M.R., Doetsch, P.W., and Deutsch, W.A., EMBO J., 1996, vol. 15, pp. 2306–2312.

  6. 6

    Deutsch, W.A., Yacoub, A., Jaruga, P., Zastawny, T.H., and Dizdaroglu, M., J. Biol. Chem., 1997, vol. 272, pp. 32 857–32 860.

  7. 7

    Wilson, IIID.M., Deutsch, W.A., and Kelley, M.R., Nucleic Acids Res., 1993, vol. 21, p. 2516.

  8. 8

    Sandigursky, M., Yacoub, A., Kelley, M.R., Deutsch, W.A., and Franklin, W.A., J. Biol. Chem., 1997, vol. 272, pp. 17 480–17 484.

  9. 9

    Kim, J., Chubatsu, L.S., Admon, A., Stahl, J., Fellous, R., and Linn, S., J. Biol. Chem., 1995, vol. 270, pp. 13 620–13 629.

  10. 10

    Jung, S.-O., Lee, J.Y., and Kim, J., Mol. Cells, 2001, vol. 12, pp. 84–90.

  11. 11

    Seong, K.M., Jung, S.-O., Kim, H.D., Kim, H.J., Jung, Y.-J., and Choi, S.-Y., and Kim, J., FEBS Lett., 2012, vol. 586, pp. 356–361.

  12. 12

    Grosheva, A.S., Zharkov, D.O., Stahl, J., Gopanenko, A.V., Kabilov, M.R., Graifer, D.M., and Karpova, G.G., Nucleic Acids Res., 2017, vol. 45, pp. 3833–3843.

  13. 13

    Ochkasova, A.S., Meschaninova, M.I., Venyaminova, A.G., Ivanov, A.V., Graifer, D.M., and Karpova, G.G., Biochimie, 2019, vol. 158, pp. 117–125.

  14. 14

    Fowler, C., Drinkwater, R., Skinner, J., and Burgoyne, L., Hum. Genet., 1988, vol. 79, pp. 265–272.

  15. 15

    Metzler, D.E., Biochemistry: The Chemical Reactions of Living Cells. Organization of DNA, in 2 vols., Amsterdam: Academic, 2003.

  16. 16

    Fernéndez, J.L., Vézquez-Gundin, F., Rivero, M.T., Goyanes, V., and Gosálvez, J., Mutat. Res., 2001, vol. 473, pp. 163–168.

  17. 17

    Cortés, A., Huertas, D., Marsellach, F.X., Ferrer-Miralles, N., Ortiz-Lombardia, M., Fanti, L., Pimpinelli, S., Pina, B., and Azorin, F., Genetics, 2003, vol. 117, pp. 117–125.

  18. 18

    Aze, A., Sannino, V., Soffientini, P., Bachi, A., and Costanzo, V., Nat. Cell Biol., 2016, vol. 18, pp. 684–691.

  19. 19

    Balueva, K.E., Malygin, A.A., Karpova, G.G., Nevinskii, G.A., and Zharkov, D.O., Mol. Biol., 2008, vol. 42, pp. 314–322.

Download references

Author information

Correspondence to D. M. Graifer.

Ethics declarations

Conflict of Interests

The authors state that there is no conflict of interest.

Additional information

Translated by E. Puchkov

Corresponding author: phone: +7 (383) 363-51-40; e-mail: graifer@niboch.nsc.ru; dgraifer@gmail.com.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ochkasova, A.S., Kabilov, M.R., Karpova, G.G. et al. Exploring the Interaction of Human Ribosomal Protein uS3 with Single-Stranded DNAs Having Different Sequences. Russ J Bioorg Chem 45, 619–624 (2019). https://doi.org/10.1134/S106816201906030X

Download citation

Keywords:

  • ribosomal uS3 protein
  • single-stranded DNA
  • protein binding to DNA
  • abasic site in DNA
  • AP lyase activity
  • satellite DNA