Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

The apoptosome: signalling platform of cell death

Key Points

  • Proteolytic pathways that execute apoptosis are initiated by the death-inducing signalling complex (DISC) or the apoptosome. The DISC is essentially a classic ligand-dependent transmembrane receptor complex that integrates extracellular death signals. By contrast, the apoptosome represents a soluble mechanism-based receptor platform that integrates intracellular death signals.

  • The central building block of the apoptosome is the multidomain protein Apaf-1, which consists of three fundamental units: a sensor for an apoptotic stimulus (WD40 repeats), an oligomerization unit (NB-ARC) and a domain (caspase-recruitment domain (CARD)) that recruits its target, the apical caspase-9. The NB-ARC region is homologous to the AAA+ type of ATPases, but unlike many members of this family Apaf-1 uses its ATPase function as a regulatory tool.

  • The formation of the apoptosome is dependent on cytochrome c and the nucleotide triphosphates ATP or 2′-deoxy ATP (dATP), the latter being more effective and most likely the natural agent.

  • Apaf-1 exists as a compact nucleotide-triphosphate-bound monomer, autolocked by its WD40 region. Findings from recent structural and biochemical studies can be put together to reveal the following sequence of events in apoptosome formation. First, upon the egress of the apoptotic signalling protein cytochrome c from mitochondria, it binds to the WD40 region of Apaf-1, causing hydrolysis of nucleotide triphosphate and release of the lock. Second, Apaf-1 adopts a semi-open configuration, but its nucleotide-binding and oligomerization domain (NOD; also referred to as NB-ARC) remains in an autoinhibited conformation. Third, the final opening of Apaf-1 and its subsequent oligomerization is dependent on the exchange of nucleotide diphosphate for triphosphate in the NB-ARC region of Apaf-1.

  • The functional oligomerized apoptosome is a wheel-like structure that consists of a heptameric arrangement of Apaf-1 molecules. The NB-ARC region provides the scaffold of the oligomer, whereas the CARD domains are arranged in a ring-like manner near the centre of the assembly, generating a platform competent to activate capase-9.

  • The sensor–oligomerizer–effector structure of the soluble Apaf-1 receptor is conserved in a related family of proteins, the NOD-like receptors (NLRs), which possess a domain that is closely related to the NB-ARC region of Apaf-1. These proteins, implicated in the regulation of innate immunity, can form similar soluble receptor platforms to activate their respective caspase or kinase targets.

Abstract

Recent work on the initial switches that trigger cell death has revealed surprising inventions of nature that ensure the ordered suicide of a cell that has been selected for demise. Particularly intriguing is how a signal — the release of cytochrome c from the mitochondria — is translated into the activation of the death cascade, which leads to a point of no return. Now there is new understanding of how this crucial process is delicately handled by a cytosolic signalling platform known as the apoptosome. The formation of the apoptosome and the activation of its effector, caspase-9, reveals a sophisticated mechanism that might be more common than was initially thought.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The proteolytic caspase cascade in the initiation and execution of apoptosis.
Figure 2: Caspases: architecture and activation.
Figure 3: Mechanism of apoptosome formation.
Figure 4: Shape and structure of the apoptosome.

Similar content being viewed by others

References

  1. Alnemri, E. S. et al. Human ICE/CED-3 protease nomenclature. Cell 87, 171 (1996).

    Article  CAS  Google Scholar 

  2. Timmer, J. C. & Salvesen, G. S. Caspase substrates. Cell Death Differ. 14, 66–72 (2007).

    Article  CAS  Google Scholar 

  3. LeBlanc, H. N. & Ashkenazi, A. Apo2L/TRAIL and its death and decoy receptors. Cell Death Differ. 10, 66–75 (2003).

    Article  CAS  Google Scholar 

  4. Carrington, P. E. et al. The structure of FADD and its mode of interaction with procaspase-8. Mol. Cell 22, 599–610 (2006).

    Article  CAS  Google Scholar 

  5. Yang, J. K. et al. Crystal structure of MC159 reveals molecular mechanism of DISC assembly and FLIP inhibition. Mol. Cell 20, 939–949 (2005).

    Article  CAS  Google Scholar 

  6. Li, F. Y., Jeffrey, P. D., Yu, J. W. & Shi, Y. Crystal structure of a viral FLIP: insights into FLIP-mediated inhibition of death receptor signaling. J. Biol. Chem. 281, 2960–2968 (2006).

    Article  CAS  Google Scholar 

  7. Lee, K. H. et al. The role of receptor internalization in CD95 signaling. EMBO J. 25, 1009–1023 (2006).

    Article  CAS  Google Scholar 

  8. Fuentes-Prior, P. & Salvesen, G. S. The protein structures that shape caspase activity, specificity, activation and inhibition. Biochem. J. 384, 201–232 (2004).

    Article  CAS  Google Scholar 

  9. Riedl, S. J. & Shi, Y. Molecular mechanisms of caspase regulation during apoptosis. Nature Rev. Mol. Cell Biol. 5, 897–907 (2004).

    Article  CAS  Google Scholar 

  10. Denault, J. B. et al. Engineered hybrid dimers: tracking the activation pathway of caspase-7. Mol. Cell 23, 523–533 (2006).

    Article  CAS  Google Scholar 

  11. Stennicke, H. R. et al. Caspase-9 can be activated without proteolytic processing. J. Biol. Chem. 274, 8359–8362 (1999).

    Article  CAS  Google Scholar 

  12. Rodriguez, J. & Lazebnik, Y. Caspase-9 and APAF-1 form an active holoenzyme. Genes Dev. 13, 3179–3184 (1999).

    Article  CAS  Google Scholar 

  13. Renatus, M., Stennicke, H. R., Scott, F. L., Liddington, R. C. & Salvesen, G. S. Dimer formation drives the activation of the cell death protease caspase 9. Proc. Natl Acad. Sci. USA 98, 14250–14255 (2001). Together with references 14 and 32, this paper shows that caspase-9 is activated by dimerization rather than by proteolysis.

    Article  CAS  Google Scholar 

  14. Boatright, K. M. et al. A unified model for apical caspase activation. Mol. Cell 11, 529–541 (2003).

    Article  CAS  Google Scholar 

  15. Muzio, M., Stockwell, B. R., Stennicke, H. R., Salvesen, G. S. & Dixit, V. M. An induced proximity model for caspase-8 activation. J. Biol. Chem. 273, 2926–2930 (1998).

    Article  CAS  Google Scholar 

  16. Zou, H., Henzel, W. J., Liu, X., Lutschg, A. & Wang, X. Apaf-1, a human protein homologous to C. elegans CED-4, participates in cytochrome c-dependent activation of caspase-3. Cell 90, 405–413 (1997). Reports the discovery of Apaf-1.

    Article  CAS  Google Scholar 

  17. Acehan, D. et al. Three-dimensional structure of the apoptosome: implications for assembly, procaspase-9 binding and activation. Mol. Cell 9, 423–432 (2002). Cryo-electron-microscopy structure of the human apoptosome.

    Article  CAS  Google Scholar 

  18. Riedl, S. J., Li, W., Chao, Y., Schwarzenbacher, R. & Shi, Y. Structure of the apoptotic protease-activating factor 1 bound to ADP. Nature 434, 926–933 (2005). Crystallographic structure of Apaf-1 ΔWD-40.

    Article  CAS  Google Scholar 

  19. Kim, H. E., Du, F., Fang, M. & Wang, X. Formation of apoptosome is initiated by cytochrome c-induced dATP hydrolysis and subsequent nucleotide exchange on Apaf-1. Proc. Natl Acad. Sci. USA 102, 17545–17550 (2005).

    Article  CAS  Google Scholar 

  20. Yu, X. et al. A structure of the human apoptosome at 12.8 Å resolution provides insights into this cell death platform. Structure 13, 1725–1735 (2005).

    Article  CAS  Google Scholar 

  21. Dorstyn, L. et al. The role of cytochrome c in caspase activation in Drosophila melanogaster cells. J. Cell Biol. 156, 1089–1098 (2002). Together with reference 22, this paper shows that D. melanogaster Dark, the Apaf-1 homologue, is not activated by cytochrome c.

    Article  CAS  Google Scholar 

  22. Zimmermann, K. C., Ricci, J. E., Droin, N. M. & Green, D. R. The role of ARK in stress-induced apoptosis in Drosophila cells. J. Cell Biol. 156, 1077–1087 (2002).

    Article  CAS  Google Scholar 

  23. Srinivasula, S. M., Ahmad, M., Fernandes-Alnemri, T. & Alnemri, E. S. Autoactivation of procaspase-9 by Apaf-1-mediated oligomerization. Mol. Cell 1, 949–957 (1998).

    Article  CAS  Google Scholar 

  24. Hu, Y., Ding, L., Spencer, D. M. & Nuñez, G. WD-40 repeat region regulates Apaf-1 self-association and procaspase-9 activation. J. Biol. Chem. 273, 33489–33494 (1998). Demonstration that Apaf-1 ΔWD-40 is constitutively active without cytochrome c.

    Article  CAS  Google Scholar 

  25. Qin, H. et al. Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1. Nature 399, 549–557 (1999).

    Article  CAS  Google Scholar 

  26. Hanson, P. I. & Whiteheart, S. W. AAA+ proteins: have engine, will work. Nature Rev. Mol. Cell Biol. 6, 519–529 (2005).

    CAS  Google Scholar 

  27. Hu, Y., Benedict, M. A., Ding, L. & Nuñez, G. Role of cytochrome c and dATP/ATP hydrolysis in Apaf-1-mediated caspase-9 activation and apoptosis. EMBO J. 18, 3586–3595 (1999).

    Article  CAS  Google Scholar 

  28. Li, P. et al. Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade. Cell 91, 479–489 (1997). Discovery that caspase-9 is the target protease of Apaf-1.

    Article  CAS  Google Scholar 

  29. Saleh, A., Srinivasula, S. M., Acharya, S., Fishel, R. & Alnemri, E. S. Cytochrome c and dATP-mediated oligomerization of Apaf-1 is a prerequisite for procaspase-9 activation. J. Biol. Chem. 274, 17941–17945 (1999).

    Article  CAS  Google Scholar 

  30. Genini, D. et al. Nucleotide requirements for the in vitro activation of the apoptosis protein-activating factor-1-mediated caspase pathway. J. Biol. Chem. 275, 29–34 (2000).

    Article  CAS  Google Scholar 

  31. Diemand, A. V. & Lupas, A. N. Modeling AAA+ ring complexes from monomeric structures. J. Struct. Biol. 156, 230–243 (2006).

    Article  CAS  Google Scholar 

  32. Pop, C., Timmer, J., Sperandio, S. & Salvesen, G. S. The apoptosome activates caspase-9 by dimerization. Mol. Cell 22, 269–275 (2006).

    Article  CAS  Google Scholar 

  33. Boatright, K. M. & Salvesen, G. S. Mechanisms of caspase activation. Curr. Opin. Cell Biol. 15, 725–731 (2003).

    Article  CAS  Google Scholar 

  34. Shi, Y. Caspase activation: revisiting the induced proximity model. Cell 117, 855–858 (2004).

    Article  CAS  Google Scholar 

  35. Horvitz, H. R. Nobel lecture. Worms, life and death. Biosci. Rep. 23, 239–303 (2003).

    Article  CAS  Google Scholar 

  36. Hay, B. A. & Guo, M. Caspase-dependent cell death in Drosophila. Annu. Rev. Cell Dev. Biol. 22, 623–650 (2006).

    Article  CAS  Google Scholar 

  37. Yan, N. et al. Structure of the CED-4–CED-9 complex reveals insights into programmed cell death in Caenorhabditis elegans. Nature 437, 831–837 (2005). Crystallographic structure of CED-4, the C. elegans homologue of Apaf-1.

    Article  CAS  Google Scholar 

  38. Yu, X., Wang, L., Acehan, D., Wang, X. & Akey, C. W. Three-dimensional structure of a double apoptosome formed by the Drosophila Apaf-1 related killer. J. Mol. Biol. 355, 577–589 (2006). Cryo-electron-microscopy structure of Dark, the D. melanogaster apoptosome.

    Article  CAS  Google Scholar 

  39. Rodriguez, A. et al. Dark is a Drosophila homologue of Apaf-1/CED-4 and functions in an evolutionarily conserved death pathway. Nature Cell Biol. 1, 272–279 (1999).

    Article  CAS  Google Scholar 

  40. Martinon, F., Burns, K. & Tschopp, J. The inflammasome: a molecular platform triggering activation of inflammatory caspases and processing of proIL-β. Mol. Cell 10, 417–426 (2002). First description of the inflammasome.

    Article  CAS  Google Scholar 

  41. Martinon, F. & Tschopp, J. NLRs join TLRs as innate sensors of pathogens. Trends Immunol. 26, 447–454 (2005).

    Article  CAS  Google Scholar 

  42. Inohara, N., Chamaillard, H., McDonald, C. & Nuñez, G. NOD-LRR proteins: role in host-microbial interactions and inflammatory disease. Annu. Rev. Biochem. 74, 355–383 (2005).

    Article  CAS  Google Scholar 

  43. Ogura, Y., Sutterwala, F. S. & Flavell, R. A. The inflammasome: first line of the immune response to cell stress. Cell 126, 659–662 (2006).

    Article  CAS  Google Scholar 

  44. Reed, J. C. et al. Comparative analysis of apoptosis and inflammation genes of mice and humans. Genome Res. 13, 1376–1388 (2003).

    CAS  Google Scholar 

  45. Ting, J. P., Kastner, D. L. & Hoffman, H. M. CATERPILLERs, pyrin and hereditary immunological disorders. Nature Rev. Immunol. 6, 183–195 (2006).

    Article  CAS  Google Scholar 

  46. Meylan, E., Tschopp, J. & Karin, M. Intracellular pattern recognition receptors in the host response. Nature 442, 39–44 (2006).

    Article  CAS  Google Scholar 

  47. Tschopp, J., Martinon, F. & Burns, K. NALPs: a novel protein family involved in inflammation. Nature Rev. Mol. Cell Biol. 4, 95–104 (2003).

    Article  CAS  Google Scholar 

  48. Bao, Q., Lu, W., Rabinowitz, J. D. & Shi, Y. Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1. Mol. Cell 25, 181–192 (2007).

    Article  CAS  Google Scholar 

  49. Seiffert, B. M., Vier, J. & Hacker, G. Subcellular localization, oligomerization, and ATP-binding of Caenorhabditis elegans CED-4. Biochem. Biophys. Res. Commun. 290, 359–365 (2002).

    Article  CAS  Google Scholar 

  50. Ogura, T., Whiteheart, S. W. & Wilkinson, A. J. Conserved arginine residues implicated in ATP hydrolysis, nucleotide-sensing, and inter-subunit interactions in AAA and AAA+ ATPases. J. Struct. Biol. 146, 106–112 (2004).

    Article  CAS  Google Scholar 

  51. Beere, H. M. et al. Heat-shock protein 70 inhibits apoptosis by preventing recruitment of procaspase-9 to the Apaf-1 apoptosome. Nature Cell Biol. 2, 469–475 (2000).

    Article  CAS  Google Scholar 

  52. Jiang, X. et al. Distinctive roles of PHAP proteins and prothymosin-α in a death regulatory pathway. Science 299, 223–226 (2003).

    Article  CAS  Google Scholar 

  53. Pan, G., O'Rourke, K. & Dixit, V. M. Caspase-9, Bcl-XL, and Apaf-1 form a ternary complex. J. Biol. Chem. 273, 5841–5845 (1998).

    Article  CAS  Google Scholar 

  54. Chau, B. N., Cheng, E. H., Kerr, D. A. & Hardwick, J. M. Aven, a novel inhibitor of caspase activation, binds Bcl-xL and Apaf-1. Mol. Cell 6, 31–40 (2000).

    Article  CAS  Google Scholar 

  55. Cho, D. H. et al. Suppression of hypoxic cell death by APIP-induced sustained activation of AKT and ERK1/2. Oncogene 6 Nov 2006 (doi: 10.1038/sj.onc.1210080).

  56. Ammelburg, M., Frickey, T. & Lupas, A. N. Classification of AAA+ proteins. J. Struct. Biol. 156, 2–11 (2006).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank C. Akey for kindly providing images of the apoptosome as well as the model of the apoptosome, and we thank J. Heuser for the electron-microscopy image of the locked apoptosome. We also thank A. Lupas and A. Diemand for providing the coordinates for the AAA+-like model of the apoptosome. Further thanks go to current or former members of our laboratories and colleagues, for their support and advice. We apologize to our colleagues whose important contributions were inadvertently overlooked or cited only indirectly due to space limitations. S.J.R. is a fellow of the Leukemia and Lymphoma Society and the V Foundation.

Author information

Authors and Affiliations

Authors

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

Related links

DATABASES

Protein Data Bank

1F1J

1GQF

1JXQ

1NY6

1Z6T

FURTHER INFORMATION

Stefan J. Riedl's homepage

Guy S. Salvesen's homepage

Glossary

Zymogen

Pro-form or precursor of an enzyme. In the context of this review, refers to the latent form of a caspase before its activation.

Extrinsic pathway

Apoptotic pathway that initiates cell death following an extracellular signal. Binding of a death ligand to a death receptor triggers the formation of the death-inducing signalling complex (DISC). This leads to caspase-8 (or caspase-10) activation and subsequent caspase-3 activation and cell death.

Death-inducing signalling complex

A group of cellular factors that are recruited to the intracellular domain of the cell-surface receptor CD95/Fas/Apo-1 after ligand binding.

Intrinsic pathway

Apoptotic pathway that initiates cell death following an intracellular signal. Stress signals from within the cell lead to the release of mitochondrial factors, among them cytochrome c. This triggers apoptosome formation, leading to caspase-9 activation and subsequent caspase-3 activation and cell death.

AAA+

Extended superfamily of ATPases associated with a variety of cellular activities. Characterized by their extended P-loop ATPase domain that is capable of forming ring-like oligomers.

Caspase-recruitment domain

(CARD). Similar to the pyrin domain, a small helical death domain that is involved in protein–protein interactions. The CARD is vital for the interaction of Apaf-1 with caspase-9; it is also found in several nucleotide-binding and oligomerization domain (NOD)-like receptors and other caspases.

WD40 repeat

A repeat sequence of 40 amino acids, which often terminates in Trp–Asp. WD40 repeats form circular β-propeller structures that are implicated in various functions by building the scaffold for protein–protein interactions.

Winged-helix domain

A motif usually found in DNA-binding proteins. In Apaf-1, the winged-helix domain directly interacts with the bound ADP of the autoinhibited state. Here, the winged-helix domain might have a role in sensing the bound nucleotide. It is a key structural element for the transformation of the autoinhibited state of Apaf-1 into the apoptosome.

Superhelical domain

In Apaf-1, several helices form a higher-order structure, which is referred to as a superhelical domain, similar to those found in Armadillo-repeat proteins.

Toll-like receptor family

Family of transmembrane receptors with a central role in the innate immune system. They are important sensors of pathogen-associated molecular patterns (PAMPs) and trigger the induction of inflammatory responses.

Leu-rich repeats

Consist of several repeats of a 20–30 amino-acid motif, which show conserved patterns containing Leu residues. These repeats form horseshoe-like structures that serve various functions including protein–protein interaction and pathogen recognition.

Pyrin domain

Globular α-helical domain that belongs to the 'DEATH fold'. A protein–protein interaction domain that is found in several nucleotide-binding and oligomerization domain (NOD)-like receptors. The DEATH fold refers to a structural motif present in several proteins that regulate apoptosis or inflammation. Examples include the death domain, death effector domain, caspase-recruitment domain and pyrin domain, each of which acts as a recruitment module for the formation of higher-order complexes.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Riedl, S., Salvesen, G. The apoptosome: signalling platform of cell death. Nat Rev Mol Cell Biol 8, 405–413 (2007). https://doi.org/10.1038/nrm2153

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm2153

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing