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Direct characterization of E2-dependent target specificity and processivity using an artificial p27-linker-E2 ubiquitination system

  • Ryu, Kyoung-Seok (Magnetic Resonance Team, Korea Basic Science Institute) ;
  • Choi, Yun-Seok (Magnetic Resonance Team, Korea Basic Science Institute) ;
  • Ko, Jun-Sang (Department of Chemistry and National Creative Research Initiative Center, KAIST) ;
  • Kim, Seong-Ock (Department of Chemistry and National Creative Research Initiative Center, KAIST) ;
  • Kim, Hyun-Jung (Magnetic Resonance Team, Korea Basic Science Institute) ;
  • Cheong, Hae-Kap (Magnetic Resonance Team, Korea Basic Science Institute) ;
  • Jeon, Young-Ho (Magnetic Resonance Team, Korea Basic Science Institute) ;
  • Choi, Byong-Seok (Department of Chemistry and National Creative Research Initiative Center, KAIST) ;
  • Cheong, Chae-Joon (Magnetic Resonance Team, Korea Basic Science Institute)
  • Published : 2008.12.31

Abstract

Little attention has been paid to the specificity between E2 and the target protein during ubiquitination, although RING-E3 induces a potential intra-molecular reaction by mediating the direct transfer of ubiquitin from E2 to the target protein. We have constructed artificial E2 fusion proteins in which a target protein (p27) is tethered to one of six E2s via a flexible linker. Interestingly, only three E2s (UbcH5b, hHR6b, and Cdc34) are able to ubiquitinate p27 via an intra-molecular reaction in this system. Although the first ubiquitination of p27 (p27-Ub) by Cdc34 is less efficient than that of UbcH5b and hHR6b, the additional ubiquitin attachment to p27-Ub by Cdc34 is highly efficient. The E2 core of Cdc34 provides specificity to p27, and the residues 184-196 are required for possessive ubiquitination by Cdc34. We demonstrate direct E2 specificity for p27 and also show that differential ubiquitin linkages can be dependent on E2 alone.

Keywords

References

  1. Pickart, C. M. (2004) Back to the future with ubiquitin. Cell 116, 181-190 https://doi.org/10.1016/S0092-8674(03)01074-2
  2. Brzovic, P. S., Lissounov, A., Christensen, D. E., Hoyt, D. W. and Klevit, R. E. (2006) A UbcH5/ubiquitin noncovalent complex is required for processive BRCA1- directed ubiquitination. Mol. Cell 21, 873-880 https://doi.org/10.1016/j.molcel.2006.02.008
  3. Hao, B., Zheng, N., Schulman, B. A., Wu, G., Miller, J. J., Pagano, M. and Pavletich, N. P. (2005) Structural basis of the Cks1-dependent recognition of p27(Kip1) by the SCF (Skp2) ubiquitin ligase. Mol. Cell 20, 9-19 https://doi.org/10.1016/j.molcel.2005.09.003
  4. Wu, G., Xu, G., Schulman, B. A., Jeffrey, P. D., Harper, J. W. and Pavletich, N. P. (2003) Structure of a beta-TrCP1- Skp1-beta-catenin complex: destruction motif binding and lysine specificity of the SCF (beta-TrCP1) ubiquitin ligase. Mol. Cell 11, 1445-1456 https://doi.org/10.1016/S1097-2765(03)00234-X
  5. Christensen, D. E., Brzovic, P. S. and Klevit, R. E. (2007) E2-BRCA1 RING interactions dictate synthesis of mono- or specific polyubiquitin chain linkages. Nat. Struct. Mol. Biol 14, 941-948 https://doi.org/10.1038/nsmb1295
  6. Catic, A., Collins, C., Church, G. M. and Ploegh, H. L. (2004) Preferred in vivo ubiquitination sites. Bioinformatics 20, 3302-3307 https://doi.org/10.1093/bioinformatics/bth407
  7. Shirane, M., Harumiya, Y., Ishida, N., Hirai, A., Miyamoto, C., Hatakeyama, S., Nakayama, K. and Kitagawa, M. (1999) Down-regulation of p27(Kip1) by two mechanisms, ubiquitin- mediated degradation and proteolytic processing. J. Biol. Chem. 274, 13886-13893 https://doi.org/10.1074/jbc.274.20.13886
  8. Butz, N., Ruetz, S., Natt, F., Hall, J., Weiler, J., Mestan, J., Ducarre, M., Grossenbacher, R., Hauser, P., Kempf, D. and Hofmann, F. (2005) The human ubiquitin-conjugating enzyme Cdc34 controls cellular proliferation through regulation of p27Kip1 protein levels. Exp. Cell Res. 303, 482- 493 https://doi.org/10.1016/j.yexcr.2004.10.008
  9. McKenna, S., Spyracopoulos, L., Moraes, T., Pastushok, L., Ptak, C., Xiao, W. and Ellison, M. J. (2001) Noncovalent interaction between ubiquitin and the human DNA repair protein Mms2 is required for Ubc13-mediated polyubiquitination. J. Biol. Chem. 276, 40120-40126 https://doi.org/10.1074/jbc.M102858200
  10. Matunis, M. J. (2002) On the road to repair: PCNA encounters SUMO and ubiquitin modifications. Mol. Cell 10, 441-442 https://doi.org/10.1016/S1097-2765(02)00653-6
  11. Pickart, C. M. (2001) Mechanisms underlying ubiquitination. Annu. Rev. Biochem. 70, 503-533 https://doi.org/10.1146/annurev.biochem.70.1.503
  12. Wu, K., Chen, A., Tan, P. and Pan, Z. Q. (2002) The Nedd8-conjugated ROC1-CUL1 core ubiquitin ligase utilizes Nedd8 charged surface residues for efficient polyubiquitin chain assembly catalyzed by Cdc34. J. Biol. Chem. 277, 516-527 https://doi.org/10.1074/jbc.M108008200
  13. Peng, J., Schwartz, D., Elias, J. E., Thoreen, C. C., Cheng, D., Marsischky, G., Roelofs, J., Finley, D. and Gygi, S. P. (2003) A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 21, 921-926 https://doi.org/10.1038/nbt849
  14. Peng, J. (2008) Evaluation of proteomic strategies for analyzing ubiquitinated proteins. BMB Rep. 41, 177-183 https://doi.org/10.5483/BMBRep.2008.41.3.177
  15. Melchior, F., Schergaut, M. and Pichler, A. (2003) SUMO: ligases, isopeptidases and nuclear pores. Trends Biochem. Sci. 28, 612-618 https://doi.org/10.1016/j.tibs.2003.09.002
  16. Lin, D., Tatham, M. H., Yu, B., Kim, S., Hay, R. T. and Chen, Y. (2002) Identification of a substrate recognition site on Ubc9. J. Biol. Chem. 277, 21740-21748 https://doi.org/10.1074/jbc.M108418200
  17. Ha, B. H. and Kim, E. E. (2008) Structures of proteases for ubiqutin and ubiquitin-like modifiers. BMB Rep. 41, 435-443 https://doi.org/10.5483/BMBRep.2008.41.6.435
  18. Seol, J. H., Feldman, R. M., Zachariae, W., Shevchenko, A., Correll, C. C., Lyapina, S., Chi, Y., Galova, M., Claypool, J., Sandmeyer, S., Nasmyth, K. and Deshaies, R. J. (1999) Cdc53/cullin and the essential Hrt1 RING-H2 subunit of SCF define a ubiquitin ligase module that activates the E2 enzyme Cdc34. Genes Dev. 13, 1614-1626 https://doi.org/10.1101/gad.13.12.1614
  19. Oh, K. J., Kalinina, A., Wang, J., Nakayama, K., Nakayama, K. I. and Bagchi, S. (2004) The papillomavirus E7 oncoprotein is ubiquitinated by UbcH7 and Cullin 1- and Skp2-containing E3 ligase. J. Virol. 78, 5338-5346 https://doi.org/10.1128/JVI.78.10.5338-5346.2004
  20. Brzovic, P. S., Keeffe, J. R., Nishikawa, H., Miyamoto, K., Fox, D., 3rd, Fukuda, M., Ohta, T. and Klevit, R. (2003) Binding and recognition in the assembly of an active BRCA1/BARD1 ubiquitin-ligase complex. Proc. Natl. Acad. Sci. U.S.A. 100, 5646-5651
  21. Petroski, M. D. and Deshaies, R. J. (2005) Mechanism of lysine 48-linked ubiquitin-chain synthesis by the cullin- RING ubiquitin-ligase complex SCF-Cdc34. Cell 123, 1107-1120 https://doi.org/10.1016/j.cell.2005.09.033
  22. Rodrigo-Brenni, M. C. and Morgan, D. O. (2007) Sequential E2s drive polyubiquitin chain assembly on APC targets. Cell 130, 127-139 https://doi.org/10.1016/j.cell.2007.05.027
  23. Hochstrasser, M. (1996) Ubiquitin-dependent protein degradation. Annu. Rev. Genet. 30, 405-439 https://doi.org/10.1146/annurev.genet.30.1.405
  24. VanDemark, A. P., Hofmann, R. M., Tsui, C., Pickart, C. M. and Wolberger, C. (2001) Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer. Cell 105, 711-720 https://doi.org/10.1016/S0092-8674(01)00387-7
  25. Kirkpatrick, D. S., Hathaway, N. A., Hanna, J., Elsasser, S., Rush, J., Finley, D., King, R. W. and Gygi, S. P. (2006) Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology. Nat. Cell Biol. 8, 700-710 https://doi.org/10.1038/ncb1436
  26. Tan, P., Fuchs, S. Y., Chen, A., Wu, K., Gomez, C., Ronai, Z. and Pan, Z. Q. (1999) Recruitment of a ROC1-CUL1 ubiquitin ligase by Skp1 and HOS to catalyze the ubiquitination of I kappa B alpha. Mol. Cell 3, 527-533 https://doi.org/10.1016/S1097-2765(00)80481-5

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