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Order of the Proteasomal ATPases and Eukaryotic Proteasome Assembly

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Abstract

The 26S proteasome is responsible for a large fraction of the regulated protein degradation in eukaryotic cells. The enzyme complex is composed of a 20S proteolytic core particle (CP) capped on one or both ends with a 19S regulatory particle (RP). The RP recognizes and unfolds substrates and translocates them into the CP. The RP can be further divided into lid and base subcomplexes. The base contains a ring of six AAA+ ATPases (Rpts) that directly abuts the CP and is responsible for unfolding substrates and driving them into the CP for proteolysis. Although 120 arrangements of the six different ATPases within the ring are possible in principle, they array themselves in one specific order. The high sequence and structural similarity between the Rpt subunits presents special challenges for their ordered association and incorporation into the assembling proteasome. In this review, we discuss recent advances in our understanding of proteasomal RP base biogenesis, with emphasis on potential specificity determinants in ring arrangement, and the implications of the ATPase ring arrangement for proteasome assembly.

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References

  1. Finley, D. (2009). Recognition and processing of ubiquitin–protein conjugates by the proteasome. Annual Review of Biochemistry, 78, 477–513.

    Article  PubMed  CAS  Google Scholar 

  2. Kerscher, O., Felberbaum, R., & Hochstrasser, M. (2006). Modification of proteins by ubiquitin and ubiquitin-like proteins. Annual Review of Cell Developmental Biology, 22, 159–180.

    Article  CAS  Google Scholar 

  3. Elsasser, S., & Finley, D. (2005). Delivery of ubiquitinated substrates to protein-unfolding machines. Nature Cell Biology, 7, 742–749.

    Article  PubMed  CAS  Google Scholar 

  4. Pickart, C. M., & Cohen, R. E. (2004). Proteasomes and their kin: Proteases in the machine age. Nature Review Molecular Cell Biology, 5, 177–187.

    Article  CAS  Google Scholar 

  5. Hochstrasser, M., & Wang, J. (2001). Unraveling the means to the end in ATP-dependent proteases. Nature Structural Biology, 8, 294–296.

    Article  PubMed  CAS  Google Scholar 

  6. Glickman, M. H., Rubin, D. M., Coux, O., Wefes, I., Pfeifer, G., Cjeka, Z., et al. (1998). A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9-signalosome and eIF3. Cell, 94, 615–623.

    Article  PubMed  CAS  Google Scholar 

  7. Tomko, R. J., Jr., Funakoshi, M., Schneider, K., Wang, J., & Hochstrasser, M. (2010). Heterohexameric ring arrangement of the eukaryotic proteasomal ATPases: Implications for proteasome structure and assembly. Molecular Cell, 38, 393–403.

    Article  PubMed  CAS  Google Scholar 

  8. Zwickl, P., Kleinz, J., & Baumeister, W. (1994). Critical elements in proteasome assembly. Nature Structural Biology, 1, 765–770.

    Article  PubMed  CAS  Google Scholar 

  9. Mayr, J., Seemuller, E., Muller, S. A., Engel, A., & Baumeister, W. (1998). Late events in the assembly of 20S proteasomes. Journal of Structural Biology, 124, 179–188.

    Article  PubMed  CAS  Google Scholar 

  10. Chen, P., & Hochstrasser, M. (1996). Autocatalytic subunit processing couples active site formation in the 20S proteasome to completion of assembly. Cell, 86, 961–972.

    Article  PubMed  CAS  Google Scholar 

  11. Kwon, Y. D., Nagy, I., Adams, P. D., Baumeister, W., & Jap, B. K. (2004). Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly. Journal of Molecular Biology, 335, 233–245.

    Article  PubMed  CAS  Google Scholar 

  12. Zuhl, F., Seemuller, E., Golbik, R., & Baumeister, W. (1997). Dissecting the assembly pathway of the 20S proteasome. FEBS Letter, 418, 189–194.

    Article  CAS  Google Scholar 

  13. Sharon, M., Witt, S., Glasmacher, E., Baumeister, W., & Robinson, C. V. (2007). Mass spectrometry reveals the missing links in the assembly pathway of the bacterial 20 S proteasome. The Journal of Biological Chemistry, 282, 18448–18457.

    Article  PubMed  CAS  Google Scholar 

  14. Djuranovic, S., Hartmann, M. D., Habeck, M., Ursinus, A., Zwickl, P., Martin, J., et al. (2009). Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases. Molecular Cell, 34, 580–590.

    Article  PubMed  CAS  Google Scholar 

  15. Wolf, S., Nagy, I., Lupas, A., Pfeifer, G., Cejka, Z., Muller, S. A., et al. (1998). Characterization of ARC, a divergent member of the AAA ATPase family from Rhodococcus erythropolis. Journal of Molecular Biology, 277, 13–25.

    Article  PubMed  CAS  Google Scholar 

  16. Zhang, F., Hu, M., Tian, G., Zhang, P., Finley, D., Jeffrey, P. D., et al. (2009). Structural insights into the regulatory particle of the proteasome from Methanocaldococcus jannaschii. Molecular Cell, 34, 473–484.

    Article  PubMed  Google Scholar 

  17. Zwickl, P., Ng, D., Woo, K. M., Klenk, H. P., & Goldberg, A. L. (1999). An archaebacterial ATPase, homologous to ATPases in the eukaryotic 26 S proteasome, activates protein breakdown by 20 S proteasomes. The Journal of Biological Chemistry, 274, 26008–26014.

    Article  PubMed  CAS  Google Scholar 

  18. Rabl, J., Smith, D. M., Yu, Y., Chang, S. C., Goldberg, A. L., & Cheng, Y. (2008). Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases. Molecular Cell, 30, 360–368.

    Article  PubMed  CAS  Google Scholar 

  19. Zhang, F., Wu, Z., Zhang, P., Tian, G., Finley, D., & Shi, Y. (2009). Mechanism of substrate unfolding and translocation by the regulatory particle of the proteasome from Methanocaldococcus jannaschii. Molecular Cell, 34, 485–496.

    Article  PubMed  CAS  Google Scholar 

  20. Gerards, W. L., Enzlin, J., Haner, M., Hendriks, I. L., Aebi, U., Bloemendal, H., et al. (1997). The human alpha-type proteasomal subunit HsC8 forms a double ringlike structure, but does not assemble into proteasome-like particles with the beta-type subunits HsDelta or HsBPROS26. The Journal of Biological Chemistry, 272, 10080–10086.

    Article  PubMed  CAS  Google Scholar 

  21. Gerards, W. L., de Jong, W. W., Bloemendal, H., & Boelens, W. (1998). The human proteasomal subunit HsC8 induces ring formation of other alpha-type subunits. Journal of Molecular Biology, 275, 113–121.

    Article  PubMed  CAS  Google Scholar 

  22. Velichutina, I., Connerly, P. L., Arendt, C. S., Li, X., & Hochstrasser, M. (2004). Plasticity in eucaryotic 20S proteasome ring assembly revealed by a subunit deletion in yeast. The EMBO Journal, 23, 500–510.

    Article  PubMed  CAS  Google Scholar 

  23. Kusmierczyk, A. R., Kunjappu, M. J., Funakoshi, M., & Hochstrasser, M. (2008). A multimeric assembly factor controls the formation of alternative 20S proteasomes. Nature Structural and Molecular Biology, 15, 237–244.

    Article  PubMed  CAS  Google Scholar 

  24. Takeuchi, J., & Tamura, T. (2004). Recombinant ATPases of the yeast 26S proteasome activate protein degradation by the 20S proteasome. FEBS Letter, 565, 39–42.

    Article  CAS  Google Scholar 

  25. Yashiroda, H., Mizushima, T., Okamoto, K., Kameyama, T., Hayashi, H., Kishimoto, T., et al. (2008). Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes. Nature Structural and Molecular Biology, 15, 228–236.

    Article  PubMed  CAS  Google Scholar 

  26. Ramos, P. C., Hockendorff, J., Johnson, E. S., Varshavsky, A., & Dohmen, R. J. (1998). Ump1p is required for proper maturation of the 20S proteasome and becomes its substrate upon completion of the assembly. Cell, 92, 489–499.

    Article  PubMed  CAS  Google Scholar 

  27. Li, X., Kusmierczyk, A. R., Wong, P., Emili, A., & Hochstrasser, M. (2007). beta-Subunit appendages promote 20S proteasome assembly by overcoming an Ump1-dependent checkpoint. The EMBO Journal, 26, 2339–2349.

    Article  PubMed  CAS  Google Scholar 

  28. Funakoshi, M., Tomko, R. J., Jr., Kobayashi, H., & Hochstrasser, M. (2009). Multiple assembly chaperones govern biogenesis of the proteasome regulatory particle base. Cell, 137, 887–899.

    Article  PubMed  CAS  Google Scholar 

  29. Kaneko, T., Hamazaki, J., Iemura, S., Sasaki, K., Furuyama, K., Natsume, T., et al. (2009). Assembly pathway of the Mammalian proteasome base subcomplex is mediated by multiple specific chaperones. Cell, 137, 914–925.

    Article  PubMed  CAS  Google Scholar 

  30. Saeki, Y., Toh, E. A., Kudo, T., Kawamura, H., & Tanaka, K. (2009). Multiple proteasome-interacting proteins assist the assembly of the yeast 19S regulatory particle. Cell, 137, 900–913.

    Article  PubMed  CAS  Google Scholar 

  31. Park, S., Roelofs, J., Kim, W., Robert, J., Schmidt, M., Gygi, S. P., et al. (2009). Hexameric assembly of the proteasomal ATPases is templated through their C termini. Nature, 459, 866–870.

    Article  PubMed  CAS  Google Scholar 

  32. Roelofs, J., Park, S., Haas, W., Tian, G., McAllister, F. E., Huo, Y., et al. (2009). Chaperone-mediated pathway of proteasome regulatory particle assembly. Nature, 459, 861–865.

    Article  PubMed  CAS  Google Scholar 

  33. Thompson, D., Hakala, K., & De Martino, G. N. (2009). Subcomplexes of PA700, the 19 S regulator of the 26 S proteasome, reveal relative roles of AAA subunits in 26 S proteasome assembly and activation and ATPase activity. The Journal of Biological Chemistry, 284, 24891–24903.

    Article  PubMed  CAS  Google Scholar 

  34. Hendil, K. B., Kriegenburg, F., Tanaka, K., Murata, S., Lauridsen, A. M., Johnsen, A. H., et al. (2009). The 20S proteasome as an assembly platform for the 19S regulatory complex. Journal of Molecular Biology, 394, 320–328.

    Article  PubMed  CAS  Google Scholar 

  35. Isono, E., Nishihara, K., Saeki, Y., Yashiroda, H., Kamata, N., Ge, L., et al. (2007). The assembly pathway of the 19S regulatory particle of the yeast 26S proteasome. Molecular Biology of the Cell, 18, 569–580.

    Article  PubMed  CAS  Google Scholar 

  36. Le Tallec, B., Barrault, M. B., Guerois, R., Carre, T., & Peyroche, A. (2009). Hsm3/S5b participates in the assembly pathway of the 19S regulatory particle of the proteasome. Molecular Cell, 33, 389–399.

    Article  PubMed  CAS  Google Scholar 

  37. Glickman, M. H., Rubin, D. M., Fried, V. A., & Finley, D. (1998). The regulatory particle of the Saccharomyces cerevisiae proteasome. Molecular and Cellular Biology, 18, 3149–3162.

    PubMed  CAS  Google Scholar 

  38. Bochtler, M., Hartmann, C., Song, H. K., Bourenkov, G. P., Bartunik, H. D., & Huber, R. (2000). The structures of HsIU and the ATP-dependent protease HsIU-HsIV. Nature, 403, 800–805.

    Article  PubMed  CAS  Google Scholar 

  39. Forster, F., Lasker, K., Beck, F., Nickell, S., Sali, A., & Baumeister, W. (2009). An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome. Biochemical and Biophysical Research Communications, 388, 228–233.

    Article  PubMed  Google Scholar 

  40. Nickell, S., Beck, F., Scheres, S. H., Korinek, A., Forster, F., Lasker, K., et al. (2009). Insights into the molecular architecture of the 26S proteasome. Proceedings of the National Academy Science of the United States of America, 106, 11943–11947.

    Article  CAS  Google Scholar 

  41. Kim, D. Y., & Kim, K. K. (2003). Crystal structure of ClpX molecular chaperone from Helicobacter pylori. The Journal of Biological Chemistry, 278, 50664–50670.

    Article  PubMed  CAS  Google Scholar 

  42. Nakamura, Y., Umehara, T., Tanaka, A., Horikoshi, M., Padmanabhan, B., & Yokoyama, S. (2007). Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome. Biochemical and Biophysical Research Communications, 359, 503–509.

    Article  PubMed  CAS  Google Scholar 

  43. Effantin, G., Rosenzweig, R., Glickman, M. H., & Steven, A. C. (2009). Electron microscopic evidence in support of alpha-solenoid models of proteasomal subunits Rpn1 and Rpn2. Journal of Molecular Biology, 386, 1204–1211.

    Article  PubMed  CAS  Google Scholar 

  44. Richmond, C., Gorbea, C., & Rechsteiner, M. (1997). Specific interactions between ATPase subunits of the 26 S protease. The Journal of Biological Chemistry, 272, 13403–13411.

    Article  PubMed  CAS  Google Scholar 

  45. Gillette, T. G., Kumar, B., Thompson, D., Slaughter, C. A., & DeMartino, G. N. (2008). Differential roles of the COOH termini of AAA subunits of PA700 (19 S regulator) in asymmetric assembly and activation of the 26 S proteasome. The Journal of Biological Chemistry, 283, 31813–31822.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The authors wish to thank Mary J. Kunjappu and Eric M. Rubenstein for comments on the manuscript. This study was supported by a National Institutes of Health grant (R01 GM083050) to MH. RJT Jr. was supported in part by an American Cancer Society New England Division—Mass Biotech Council Cancer Research Challenge—Millennium: The Takeda Oncology Company Postdoctoral Fellowship.

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Correspondence to Mark Hochstrasser.

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Tomko, R.J., Hochstrasser, M. Order of the Proteasomal ATPases and Eukaryotic Proteasome Assembly. Cell Biochem Biophys 60, 13–20 (2011). https://doi.org/10.1007/s12013-011-9178-4

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