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The linker connecting the tandem ubiquitin binding domains of RAP80 is critical for lysine 63-linked polyubiquitin-dependent binding activity

  • Cho, Hyun-Jung (Department of Biological Science, Sungkyunkwan University) ;
  • Lee, Sang-Ho (Department of Biological Science, Sungkyunkwan University) ;
  • Kim, Hong-Tae (Department of Biological Science, Sungkyunkwan University)
  • Published : 2009.11.30

Abstract

The tandem ubiquitin-interacting motif (UIM) domain located at the N-terminus of Receptor Associated Protein 80 (RAP80) plays a crucial role in ionizing radiation (IR)-induced DNA damage response. RAP80 translocates to sites of IR-induced DNA damage through interaction of its UIM domain with ubiquitinated H2A and Lys63-linked polyubiquitin chains. The exact mechanism, however, through which RAP80 associates with Lys63-linked polyubiquitin chains is not clear. Here, we show by in vitro GST-pull down assays that modifying the linker region between the tandem ubiquitin binding domains of RAP80 changes the binding affinity for Lys63-linked polyubiquitin chains and affects translocation to sites of DNA breaks. Based on these findings, we suggest that the length of the linker region between the tandem ubiquitin binding domains of RAP80 may be a key factor in the binding of RAP80 with Lys63-linked polyubiquitin chains as well as in the translocation of RAP80 to DNA break sites.

Keywords

References

  1. Rouse, J. and Jackson, S. P. (2002) Interfaces between the detection, signaling, and repair of DNA damage. Science 297, 547-551 https://doi.org/10.1126/science.1074740
  2. Su, T. T. (2006) Cellular responses to DNA damage: one signal, multiple choices. Annu. Rev. Genet. 40, 187-208 https://doi.org/10.1146/annurev.genet.40.110405.090428
  3. Kim, H. and Chen, J. (2008) New players in the BRCA1-mediated DNA damage responsive pathway. Mol. Cells 25, 457-461
  4. Kim, H., Huang, J. and Chen, J. (2007) CCDC98 is a BRCA1-BRCT domain-binding protein involved in the DNA damage response. Nat. Struct. Mol. Biol. 14,710-715 https://doi.org/10.1038/nsmb1277
  5. Liu, Z., Wu, J. and Yu, X. (2007) CCDC98 targets BRCA1 to DNA damage sites. Nat. Struct. Mol. Biol. 14, 716-720 https://doi.org/10.1038/nsmb1279
  6. Yan, J., Kim, Y. S., Yang, X. P., Li, L. P., Liao, G., Xia, F. and Jetten, A. M. (2007) The ubiquitin-interacting motif containing protein RAP80 interacts with BRCA1 and functions in DNA damage repair response. Cancer Res. 67, 6647-6656 https://doi.org/10.1158/0008-5472.CAN-07-0924
  7. Kim, H., Chen, J. and Yu, X. (2007) Ubiquitin-binding protein RAP80 mediates BRCA1-dependent DNA damage response. Science 316, 1202-1205 https://doi.org/10.1126/science.1139621
  8. Sobhian, B., Shao, G., Lilli, D. R., Culhane, A. C., Moreau, L. A., Xia, B., Livingston, D. M. and Greenberg, R. A. (2007) RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites. Science 316, 1198-1202 https://doi.org/10.1126/science.1139516
  9. Wang, B., Matsuoka, S., Ballif, B. A., Zhang, D., Smogorzewska, A., Gygi, S. P. and Elledge, S. J. (2007) Abraxas and RAP80 form a BRCA1 protein complex required for the DNA damage response. Science 316, 1194-1198 https://doi.org/10.1126/science.1139476
  10. Wang, B. and Elledge, S. J. (2007) Ubc13/Rnf8 ubiquitin ligases control foci formation of the Rap80/Abraxas/Brca1/Brcc36 complex in response to DNA damage. Proc. Natl. Acad. Sci. U.S.A. 104, 20759-20763 https://doi.org/10.1073/pnas.0710061104
  11. Hjerpe, R. and Rodriguez, M. S. (2008) Efficient approaches for characterizing ubiquitinated proteins. Biochem. Soc. Trans. 36, 823-827 https://doi.org/10.1042/BST0360823
  12. Bilodeau, P. S., Urbanowski, J. L., Winistorfer, S. C. and Piper, R. C. (2002) The Vps27p Hse1p complex binds ubiquitin and mediates endosomal protein sorting. Nat. Cell Biol. 4, 534-539
  13. Howarth, J. L., Kelly, S., Keasey, M. P., Glover, C. P., Lee, Y. B., Mitrophanous, K., Chapple, J. P., Gallo, J. M., Cheetham, M. E. and Uney, J. B. (2007) Hsp40 molecules that target to the ubiquitin-proteasome system decrease inclusion formation in models of polyglutamine disease. Mol. Ther. 15, 1100-1105
  14. Uchiki, T., Kim, H. T., Zhai, B., Gygi, S. P., Johnston, J. A., O'Bryan, J. P. and Goldberg, A. L. (2009) The Ubiquitin-interacting Motif Protein, S5a, Is Ubiquitinated by All Types of Ubiquitin Ligases by a Mechanism Different from Typical Substrate Recognition. J. Biol. Chem. 284, 12622-12632 https://doi.org/10.1074/jbc.M900556200
  15. Hirano, S., Kawasaki, M., Ura, H., Kato, R., Raiborg, C., Stenmark, H. and Wakatsuki, S. (2006) Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting. Nat. Struct. Mol. Biol. 13, 272-277 https://doi.org/10.1038/nsmb1051
  16. McCullough, J., Clague, M. J. and Urbe, S. (2004) AMSH is an endosome-associated ubiquitin isopeptidase. J. Cell. Biol. 166, 487-492 https://doi.org/10.1083/jcb.200401141
  17. Burnett, B., Li, F. and Pittman, R. N. (2003) The polyglutamine neurodegenerative protein ataxin-3 binds polyubiquitylated proteins and has ubiquitin protease activity. Hum. Mol. Genet. 12, 3195-3205 https://doi.org/10.1093/hmg/ddg344
  18. Regan-Klapisz, E., Sorokina, I., Voortman, J., de Keizer, P., Roovers, R. C., Verheesen, P., Urbe, S., Fallon, L., Fon, E. A., Verkleij, A., Benmerah, A. and van Bergen en Henegouwen, P. M. (2005) Ubiquilin recruits Eps15 into ubiquitin-rich cytoplasmic aggregates via a UIM-UBL interaction. J. Cell. Sci. 118, 4437-4450 https://doi.org/10.1242/jcs.02571
  19. Hurley, J. H., Lee, S. and Prag, G. (2006) Ubiquitin-binding domains. Biochem. J. 399, 361-372 https://doi.org/10.1042/BJ20061138
  20. Sims, J. J. and Cohen, R. E. (2009) Linkage-specific avidity defines the lysine 63-linked polyubiquitin-binding preference of rap 80. Mol. Cell. 33, 775-783
  21. Hoover, D. M. and Lubkowski, J. (2002) DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic. Acids. Res. 30, e43 https://doi.org/10.1093/nar/30.10.e43
  22. Sheffield, P., Garrard, S. and Derewenda, Z. (1999) Overcoming expression and purification problems of RhoGDI using a family of 'parallel' expression vectors. Protein Expr. Purif. 15, 34-39 https://doi.org/10.1006/prep.1998.1003

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