Skip to main content

Apoptotic Caspase Activation and Activity

  • Protocol
Apoptosis and Cancer

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 414))

Summary

Caspases are central to the execution of apoptosis. Their proteolytic activity is responsible for the demise of cells in many physiological and pathological states. Great advances in understanding caspases have been made using recombinant caspase expression and enzymatic characterization. Assays to measure caspase activity in apoptotic cell extracts and the development of a reconstituted cell-free assay were also critical in establishing the hierarchy in the caspase activation cascade and comprehend how caspase-9 is activated by the apoptosome. More recently, new tools such as activity-based probes allowed us to detect caspase activation in their working environment providing readout of the system with minimal interference. This chapter describes some of the methods used by our group to study the activation mechanisms of caspases and their activity.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Denault, J. B., and Salvesen, G. S. (2002) Caspases: keys in the ignition of cell death. Chem Rev 102, 4489–500.

    Article  CAS  PubMed  Google Scholar 

  2. Fischer, U., Janicke, R. U., and Schulze-Osthoff, K. (2003) Many cuts to ruin: a comprehensive update of caspase substrates. Cell Death Differ 10, 76–100.

    Article  CAS  PubMed  Google Scholar 

  3. Woo, E. J., Kim, Y. G., Kim, M. S., Han, W. D., Shin, S., Robinson, H., Park, S. Y., and Oh, B. H. (2004) Structural mechanism for inactivation and activation of CAD/DFF40 in the apoptotic pathway. Mol Cell 14, 531–9.

    Article  CAS  PubMed  Google Scholar 

  4. Sakahira, H., Enari, M., and Nagata, S. (1998) Cleavage of CAD inhibitor in CAD activation and DNA degradation during apoptosis. Nature 391, 96–9.

    Article  CAS  PubMed  Google Scholar 

  5. Liu, X., Zou, H., Widlak, P., Garrard, W., and Wang, X. (1999) Activation of the apoptotic endonuclease DFF40 (caspase-activated DNase or nuclease). Oligomerization and direct interaction with histone H1. J Biol Chem 274, 13836–40.

    Article  CAS  PubMed  Google Scholar 

  6. Liu, X., Zou, H., Slaughter, C., and Wang, X. (1997) DFF, a heterodimeric protein that functions downstream of caspase-3 to trigger DNA fragmentation during apoptosis. Cell 89, 175–84.

    Article  CAS  PubMed  Google Scholar 

  7. Enari, M., Sakahira, H., Yokoyama, H., Okawa, K., Iwamatsu, A., and Nagata, S. (1998) A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD. Nature 391, 43–50.

    Article  CAS  PubMed  Google Scholar 

  8. Lazebnik, Y. A., Kaufmann, S. H., Desnoyers, S., Poirier, G. G., and Earnshaw, W. C. (1994) Cleavage of poly(ADP-ribose) polymerase by a proteinase with properties like ICE. Nature 371, 346–7.

    Article  CAS  PubMed  Google Scholar 

  9. Luo, X., Budihardjo, I., Zou, H., Slaughter, C., and Wang, X. (1998) Bid, a Bcl2 interacting protein, mediates cytochrome c release from mitochondria in response to activation of cell surface death receptors. Cell 94, 481–90.

    Article  CAS  PubMed  Google Scholar 

  10. Li, H., Zhu, H., Xu, C. J., and Yuan, J. (1998) Cleavage of BID by caspase 8 mediates the mitochondrial damage in the Fas pathway of apoptosis. Cell 94, 491–501.

    Article  CAS  PubMed  Google Scholar 

  11. Cerretti, D. P., Kozlosky, C. J., Mosley, B., Nelson, N., Van Ness, K., Greenstreet, T. A., March, C. J., Kronheim, S. R., Druck, T., Cannizzaro, L. A., Huebner, K., and Black, R. A. (1992) Molecular cloning of the interleukin-1b converting enzyme. Science 256, 97–100.

    Article  CAS  PubMed  Google Scholar 

  12. Thornberry, N. A., Bull, H. G., Calaycay, J. R., Chapman, K. T., Howard, A. D., Kostura, M. J., Miller, D. K., Molineaux, S. M., Weidner, J. R., Aunins, J., Elliston, K. O., Ayala, J. M., Casano, F. J., Chin, J., Ding, G. J. F., Egger, L. A., Gaffney, E. P., Limjuco, G., Palyha, O. C., Raju, S. M., Rolando, A. M., Salley, J. P., Yamin, T. T., and Tocci, M. J. (1992) A novel heterodimeric cysteine protease is required for interleukin-1beta processing in monocytes. Nature 356, 768–74.

    Article  CAS  PubMed  Google Scholar 

  13. Alam, A., Cohen, L. Y., Aouad, S., and Sekaly, R. P. (1999) Early activation of caspases during T lymphocyte stimulation results in selective substrate cleavage in nonapoptotic cells. J Exp Med 190, 1879–90.

    Article  CAS  PubMed  Google Scholar 

  14. Kennedy, N. J., Kataoka, T., Tschopp, J., and Budd, R. C. (1999) Caspase activation is required for T cell proliferation. J Exp Med 190, 1891–6.

    Article  CAS  PubMed  Google Scholar 

  15. Algeciras-Schimnich, A., Barnhart, B. C., and Peter, M. E. (2002) Apoptosis-independent functions of killer caspases. Curr Opin Cell Biol 14, 721–6.

    Article  CAS  PubMed  Google Scholar 

  16. Fuentes-Prior, P., and Salvesen, G. S. (2004) The protein structures that shape caspase activity, specificity, activation and inhibition. Biochem J 384, 201–32.

    Article  CAS  PubMed  Google Scholar 

  17. Zhou, Q., and Salvesen, G. S. (1997) Activation of pro-caspase-7 by serine proteases includes a non-canonical specificity. Biochem J 324, 361–64.

    CAS  PubMed  Google Scholar 

  18. Boatright, K. M., Renatus, M., Scott, F. L., Sperandio, S., Shin, H., Pedersen, I., Ricci, J.-E., Edris, W. A., Sutherlin, D. P., Green, D. R., and Salvesen, G. S. (2003) A unified model for apical caspase activation. Mol Cell 11, 529–41.

    Article  CAS  PubMed  Google Scholar 

  19. Talanian, R. V., Dang, L. C., Ferenz, C. R., Hackett, M. C., Mankovich, J. A., Welch, J. P., Wong, W. W., and Brady, K. D. (1996) Stability and oligomeric equilibria of refolded interleukin-1beta converting enzyme. J Biol Chem 271, 21853–8.

    Article  CAS  PubMed  Google Scholar 

  20. Stennicke, H. R., Deveraux, Q. L., Humke, E. W., Reed, J. C., Dixit, V. M., and Salvesen, G. S. (1999) Caspase-9 can be activated without proteolytic processing. J Biol Chem 274, 8359–62.

    Article  CAS  PubMed  Google Scholar 

  21. Cowling, V., and Downward, J. (2002) Caspase-6 is the direct activator of caspase-8 in the cytochrome c-induced apoptosis pathway: absolute requirement for removal of caspase-6 prodomain. Cell Death Differ 9, 1046–56.

    Article  CAS  PubMed  Google Scholar 

  22. Pop, C., Timmer, J., Sperandio, S., and Salvesen, G. S. (2006) The apoptosome activates caspase-9 by dimerization. Mol Cell 22, 269–75.

    Article  CAS  PubMed  Google Scholar 

  23. Cain, K., Bratton, S. B., Langlais, C., Walker, G., Brown, D. G., Sun, X. M., and Cohen, G. M. (2000) Apaf-1 oligomerizes into biologically active approximately 700-kDa and inactive approximately 1.4-MDa apoptosome complexes. J Biol Chem 275, 6067–70.

    Article  CAS  PubMed  Google Scholar 

  24. Zou, H., Li, Y., Liu, X., and Wang, X. (1999) An APAF-1.cytochrome c multimeric complex is a functional apoptosome that activates procaspase-9. J Biol Chem 274, 11549–56.

    Article  CAS  PubMed  Google Scholar 

  25. Yu, X., Acehan, D., Menetret, J. F., Booth, C. R., Ludtke, S. J., Riedl, S. J., Shi, Y., Wang, X., and Akey, C. W. (2005) A structure of the human apoptosome at 12.8 A resolution provides insights into this cell death platform. Structure (Camb) 13, 1725–35.

    Article  CAS  Google Scholar 

  26. Riedl, S. J., Li, W., Chao, Y., Schwarzenbacher, R., and Shi, Y. (2005) Structure of the apoptotic protease-activating factor 1 bound to ADP. Nature 434, 926–33.

    Article  CAS  PubMed  Google Scholar 

  27. Peter, M. E., and Krammer, P. H. (2003) The CD95(APO-1/Fas) DISC and beyond. Cell Death Differ 10, 26–35.

    Article  CAS  PubMed  Google Scholar 

  28. Denault, J. B., and Salvesen, G. S. (2003) Human caspase-7 activity and regulation by its N-terminal Peptide. J Biol Chem 278, 34042–50.

    Article  CAS  PubMed  Google Scholar 

  29. Tenev, T., Zachariou, A., Wilson, R., Ditzel, M., and Meier, P. (2005) IAPs are functionally non-equivalent and regulate effector caspases through distinct mechanisms. Nat Cell Biol 7, 70–7.

    Article  CAS  PubMed  Google Scholar 

  30. Scott, F. L., Denault, J. B., Riedl, S. J., Shin, H., Renatus, M., and Salvesen, G. S. (2005) XIAP inhibits caspase-3 and -7 using two binding sites: evolutionarily conserved mechanism of IAPs. EMBO J 24, 645–55.

    Article  CAS  PubMed  Google Scholar 

  31. Riedl, S. J., Renatus, M., Schwarzenbacher, R., Zhou, Q., Sun, S., Fesik, S. W., Liddington, R. C., and Salvesen, G. S. (2001) Structural basis for the inhibition of caspase-3 by XIAP. Cell 104, 791–800.

    Article  CAS  PubMed  Google Scholar 

  32. Vaux, D. L. (1999) Caspases and apoptosis – biology and terminology. Cell Death Differ 6, 493–4.

    Article  CAS  PubMed  Google Scholar 

  33. Thornberry, N. A., Rano, T. A., Peterson, E. P., Rasper, D. M., Timkey, T., Garcia-Calvo, M., Houtzager, V. M., Nordstrom, P. A., Roy, S., Vaillancourt, J. P., Chapman, K. T., and Nicholson, D. W. (1997) A combinatorial approach defines specificities of members of the caspase family and granzyme B. Functional relationships established for key mediators of apoptosis. J Biol Chem 272, 17907–11.

    Article  CAS  PubMed  Google Scholar 

  34. Stennicke, H. R., Renatus, M., Meldal, M., and Salvesen, G. S. (2000) Internally quenched fluorescent peptide substrates disclose the subsite preferences of human caspases 1, 3, 6, 7 and 8. Biochem J 350, 563–68.

    Article  CAS  PubMed  Google Scholar 

  35. Deveraux, Q., Takahashi, R., Salvesen, G. S., and Reed, J. C. (1997) X-linked IAP is a direct inhibitor of cell death proteases. Nature 388, 300–04.

    Article  CAS  PubMed  Google Scholar 

  36. Takahashi, R., Deveraux, Q., Tamm, I., Welsh, K., Assa-Munt, N., Salvesen, G. S., and Reed, J. C. (1998) A single BIR domain of XIAP sufficient for inhibiting caspases. J Biol Chem 273, 7787–90.

    Article  CAS  PubMed  Google Scholar 

  37. Schimmer, A. D., Welsh, K., Pinilla, C., Wang, Z., Krajewska, M., Bonneau, M. J., Pedersen, I. M., Kitada, S., Scott, F. L., Bailly-Maitre, B., Glinsky, G., Scudiero, D., Sausville, E., Salvesen, G., Nefzi, A., Ostresh, J. M., Houghten, R. A., and Reed, J. C. (2004) Small-molecule antagonists of apoptosis suppressor XIAP exhibit broad antitumor activity. Cancer Cell 5, 25–35.

    Article  CAS  PubMed  Google Scholar 

  38. Schimmer, A. D., Dalili, S., Batey, R. A., and Riedl, S. J. (2006) Targeting XIAP for the treatment of malignancy. Cell Death Differ 13, 179–88.

    Article  CAS  PubMed  Google Scholar 

  39. Kato, D., Boatright, K. M., Berger, A. B., Nazif, T., Blum, G., Ryan, C., Chehade, K. A. H., Salvesen, G. S., and Bogyo, M. (2005) Activity-based probes that target diverse cysteine protease families. Nat Chem Biol 1, 33–38.

    Article  CAS  PubMed  Google Scholar 

  40. Nicholson, D. W., Ali, A., Thornberry, N. A., Vaillancourt, J. P., Ding, C. K., Gallant, M., Gareau, Y., Griffin, P. R., Labelle, M., Lazebnik, Y. A., et al. (1995) Identification and inhibition of the ICE/CED-3 protease necessary for mammalian apoptosis. Nature 376, 37–43.

    Article  CAS  PubMed  Google Scholar 

  41. Berger, A. B., Witte, M., Denault, J. B., Sagadhiani, A. M., Sexton, K. M. B., Salvesen, G. S., and Bogyo, M. (2006) Identification of early intermediates of caspase activation during intrinsic apoptosis using selective inhibitors and activity based probes. Mol Cell 23, 509–21.

    Article  CAS  PubMed  Google Scholar 

  42. Donepudi, M., Mac Sweeney, A., Briand, C., and Gruetter, M. G. (2003) Insights into the regulatory mechanism for caspase-8 activation. Mol Cell 11, 543–49.

    Article  CAS  PubMed  Google Scholar 

  43. Edelhoch, H. (1967) Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 6, 1948–54.

    Article  CAS  PubMed  Google Scholar 

  44. Stennicke, H. R., and Salvesen, G. S. (1999) Caspases: preparation and characterization. Methods 17, 313–9.

    Article  CAS  PubMed  Google Scholar 

  45. Li, P., Nijhawan, D., Budihardjo, I., Srinivasula, S. M., Ahmad, M., Alnemri, E. S., and Wang, X. (1997) Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade. Cell 91, 479–89.

    Article  CAS  PubMed  Google Scholar 

  46. Ellerby, H. M., Martin, S. J., Ellerby, L. M., Naiem, S. S., Rabizadeh, S., Salvesen, G. S., Casiano, C. A., Cashman, N. R., Green, D. R., and Bredesen, D. E. (1997) Establishment of a cell-free system of neuronal apoptosis: comparison of premitochondrial, mitochondrial, and postmitochondrial phases. J Neurosci 17, 6165–78.

    CAS  PubMed  Google Scholar 

  47. Denault, J. B., Békés, M., Scott, F. L., Sexton, K. M. B., Bogyo, M., and Salvesen, G. S. (2006) Engineered hybrid dimers: tracking the activation pathway of caspase-7. Mol Cell 23, 523–33.

    Article  CAS  PubMed  Google Scholar 

  48. Stennicke, H. R., Jurgensmeier, J. M., Shin, H., Deveraux, Q., Wolf, B. B., Yang, X., Zhou, Q., Ellerby, H. M., Ellerby, L. M., Bredesen, D., Green, D. R., Reed, J. C., Froelich, C. J., and Salvesen, G. S. (1998) Pro-caspase-3 is a major physiologic target of caspase-8. J Biol Chem 273, 27084–90.

    Article  CAS  PubMed  Google Scholar 

  49. Matsudaira, P. (1987) Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J Biol Chem 262, 10035–38.

    CAS  PubMed  Google Scholar 

  50. Schecter, I., and Berger, M. (1967) On the size of the active site in proteases. Biochem Biophys Res Commun 27, 157–62.

    Article  Google Scholar 

  51. Denault, J. -B., and Salvesen, G. S. (2002) Unit 21.13: Expression, purification and characterization of caspases, Current Protocols in Protein Sciences, John Wiley & Sons, Academic Press.

    Google Scholar 

Download references

Acknowledgments

We are grateful to the members of our laboratory who provided some of the results presented in this chapter and for carefully reviewing protocols.

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Humana Press Inc.

About this protocol

Cite this protocol

Denault, JB., Salvesen, G.S. (2008). Apoptotic Caspase Activation and Activity. In: Mor, G., Alvero, A.B. (eds) Apoptosis and Cancer. Methods in Molecular Biology™, vol 414. Humana Press. https://doi.org/10.1007/978-1-59745-339-4_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-339-4_15

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-457-9

  • Online ISBN: 978-1-59745-339-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics