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A structural view of mitochondria-mediated apoptosis

Abstract

Mitochondria-mediated apoptosis plays a central role in animal development and tissue homeostasis, and its alteration results in a range of malignant disorders including cancer. Upon apoptotic stimuli, the mitochondrial proteins cytochrome c and Smac/DIABLO are released into the cytosol, where they synergistically activate caspases by activating Apaf-1 and relieving the apoptotic inhibition by IAPs. Recent biochemical and structural studies reveal a molecular basis for these important events and identify an evolutionarily conserved mechanism of apoptosis from fruit flies to mammals.

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Figure 1: Conserved apoptotic paradigms in C. elegans, Drosophia, and mammals.
Figure 2: Recruitment of procaspase-9 by Apaf-1 through CARD–CARD interactions.
Figure 3: Smac function and a conserved IAP-binding motif.
Figure 4: Inhibition of caspases by IAP and p35.
Figure 5: Regulation of mitochondria permeability by the Bcl-2 family members.

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References

  1. Horvitz, H.R. Genetic control of programmed cell death in the nematode Caenorhabditis elegans. Cancer Res. 59, 1701–1706 (1999).

    Google Scholar 

  2. Steller, H. Mechanisms and genes of cellular suicide. Science 267, 1445–1449 (1995).

    CAS  PubMed  Google Scholar 

  3. Jacobson, M.D., Weil, M. & Raff, M.C. Programmed cell death in animal development. Cell 88, 347–354 (1997).

    CAS  PubMed  Google Scholar 

  4. Fesik, S.W. Insights into Programmed cell death through structural biology. Cell 103, 273–282 (2000).

    CAS  PubMed  Google Scholar 

  5. Thompson, C.B. Apoptosis in the pathogenesis and treatment of disease. Science 267, 1456–1462 (1995).

    Article  CAS  PubMed  Google Scholar 

  6. Green, D.R. & Martin, S.J. The killer and the executioner: how apoptosis controls malignancy. Curr. Opin. Immunol. 7, 694–703 (1995).

    CAS  PubMed  Google Scholar 

  7. Thornberry, N.A. & Lazebnik, Y. Caspases: Enemies within. Science 281, 1312–1316 (1998).

    CAS  PubMed  Google Scholar 

  8. Budihardjo, I., Oliver, H., Lutter, M., Luo, X. & Wang, X. Biochemical pathways of caspase activation during apoptosis. Annu. Rev. Cell Dev. Biol. 15, 269–290 (1999).

    CAS  PubMed  Google Scholar 

  9. Hengartner, M.O. Programmed cell death in invertebrates. Curr. Opin. Genet. Dev. 6, 34–38 (1996).

    CAS  PubMed  Google Scholar 

  10. Metzstein, M.M., Stanfield, G.M. & Horvitz, H.R. Genetics of programmed cell death in C. elegans: past, present and future. Trends Genet. 14, 410–416 (1998).

    CAS  PubMed  Google Scholar 

  11. Yang, X., Chang, H.Y. & Baltimore, D. Essential Role of CED-4 Oligomerization in CED-3 activation and apoptosis. Science 281, 1355–1357 (1998).

    CAS  PubMed  Google Scholar 

  12. 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 dctivation of caspase-3. Cell 90, 405–413 (1997).

    CAS  PubMed  Google Scholar 

  13. Li, P. et al. Cytochrome c and dATP-dependent vormation of Apaf-1/Caspase-9 complex initiates an apoptotic protease cascade. Cell 91, 479–489 (1997).

    Article  CAS  PubMed  Google Scholar 

  14. Adams, J. & Cory, S. The Bcl-2 protein family: arbiters of cell survival. Science 281, 1322–1326 (1998).

    CAS  PubMed  Google Scholar 

  15. Adams, J.M. & Cory, S. Life-or-death decisions by the Bcl-2 protein family. Trends Biochem. Sci. 26, 61–66 (2001).

    CAS  PubMed  Google Scholar 

  16. Purring, C., Zou, H., Wang, X. & McLendon, G.L. Stoichiometry, free energy, and kinetic aspects of cytochrome c:Apaf-1 binding in apoptosis. J. Am. Chem. Soc. 121, 7435–7436 (1999).

    CAS  Google Scholar 

  17. Jiang, X. & Wang, X. Cytochrome c promotes caspase-9 activation by inducing nucleotide binding to Apaf-1. J. Biol. Chem. 275, 31199–31203 (2000).

    CAS  PubMed  Google Scholar 

  18. 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).

    CAS  PubMed  Google Scholar 

  19. Hu, Y., Ding, L., Spencer, D.M. & Nunez, G. WD-40 repeat region regulates Apaf-1 self-association and rrocaspase-9 activation. J. Biol. Chem. 273, 33489–33494 (1998).

    CAS  PubMed  Google Scholar 

  20. Zou, H., Li, Y., Liu, X. & Wang, X. An APAF-1-cytochrome c multimeric complex is a functional apoptosome that activates procaspase-9. J. Biol. Chem. 274, 11549–11556 (1999).

    CAS  PubMed  Google Scholar 

  21. 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).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Srinivasula, S.M. et al. A conserved XIAP-interaction motif in caspase-9 and Smac/DIABLO mediates opposing effects on caspase activity and apoptosis. Nature 409, 112–116 (2001).

    Google Scholar 

  24. Deveraux, Q.L. & Reed, J.C. IAP family proteins — suppressors of apoptosis. Genes Dev. 13, 239–252 (1999).

    CAS  PubMed  Google Scholar 

  25. Miller, L.K. An exegesis of IAPs:salvation and surprises from BIR motifs. Trends Cell Biol. 9, 323–328 (1999).

    CAS  PubMed  Google Scholar 

  26. Chai, J. et al. Structural and biochemical basis of apoptotic activation by Smac/DIABLO. Nature 406, 855–862 (2000).

    CAS  PubMed  Google Scholar 

  27. Takahashi, R. et al. A Single BIR Domain of XIAP sufficient for inhibiting caspases. J. Biol. Chem. 273, 7787–7790 (1998).

    CAS  PubMed  Google Scholar 

  28. Sun, C. et al. NMR structure and mutagenesis of the inhibitor-of-apoptosis protein XIAP. Nature 401, 818–822 (1999).

    CAS  PubMed  Google Scholar 

  29. Sun, C. et al. NMR structure and mutagenesis of the third BIR domain of the inhibitor of apoptosis protein XIAP. J. Biol. Chem 275, 33777–33781 (2000).

    CAS  PubMed  Google Scholar 

  30. Du, C., Fang, M., Li, Y. & Wang, X. Smac, a mitochondrial protein that promotes cytochrome c-dependent caspase activation during apoptosis. Cell 102, 33–42 (2000).

    CAS  PubMed  Google Scholar 

  31. Verhagen, A.M. et al. Identification of DIABLO, a mammalian protein that promotes apoptosis by binding to and antagonizing IAP proteins. Cell 102, 43–53 (2000).

    CAS  PubMed  Google Scholar 

  32. Srinivasula, S.M. et al. Molecular determinants of the caspase-promoting activity of Smac/DIABLO and its role in the death receptor pathway. J. Biol. Chem. 275, 36152–36157 (2000).

    CAS  PubMed  Google Scholar 

  33. Bangs, P. & White, K. Regulation and execution of apoptosis during Drosophila development. Dev. Dyn. 218, 68–79 (2000).

    CAS  PubMed  Google Scholar 

  34. Kanuka, H. et al. Control of the cell death pathway by Dapaf-1, a Drosophila Apaf-1/CED-4-related caspase activator. Mol. Cell 4, 757–769 (1999).

    CAS  PubMed  Google Scholar 

  35. Zhou, L., Song, Z., Tittel, J. & Steller, H. HAC-1, a Drosophila homolog of Apaf-1 and CED-4 functions in developmental and radiation-induced apoptosis. Mol. Cell 4, 745–755 (1999).

    CAS  PubMed  Google Scholar 

  36. 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).

    CAS  PubMed  Google Scholar 

  37. Hawkins, C., Wang, S. & Hay, B.A. A cloning method to identify caspases and their regulators in yeast: identification of Drosophila IAP1 as an inhibitor of the Drosophila caspase DCP-1. Proc. Natl. Acad. Sci. USA 96, 2885–2890 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Kaiser, W., Vucic, D. & Miller, L. The Drosophila inhibitor of apoptosis DIAP1 suppresses cell death induced by the caspase drICE. FEBS Lett. 440, 243–248 (1998).

    CAS  PubMed  Google Scholar 

  39. Wang, S., Hawkins, C., Yoo, S., Muller, H.-A. & Hay, B. The Drosophila caspase inhibitor DIAP1 is essential for cell survival and is negatively regulated by HID. Cell 98, 453–463 (1999).

    CAS  PubMed  Google Scholar 

  40. Vucic, D., Kaiser, W.J. & Miller, L.K. A mutational analysis of the Baculovirus inhibitor of apoptosis Op-IAP. J. Biol. Chem. 51, 33915–33921 (1998).

    Google Scholar 

  41. Vucic, D., Kaiser, W.J. & Miller, L.K. Inhibitor of apoptosis proteins physically interact with and block apoptosis induced by Drosophila proteins HID and GRIM. Mol. Cell. Biol. 18, 3300–3309 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Vucic, D., Kaiser, W.J., Harvey, A.J. & Miller, L.K. Inhibition of reaper-induced apoptosis by interaction with inhibitior of apoptosis proteins (IAPs). Proc. Natl. Acad. Sci. USA 94, 10183–10188 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Goyal, L., McCall, K., Agapite, J., Hartwieg, E. & Steller, H. Induction of apoptosis by Drosophila reaper, hid and grim through inhibition of IAP function. EMBO J. 19, 589–597 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Hay, B.A. Understanding IAP function and regulation: a view from Drosophila. Cell Death Differ. 7, 1045–1056 (2000).

    CAS  PubMed  Google Scholar 

  45. Yoshida, H. et al. Apaf1 is required for mitochondrial pathways of apoptosis and brain development. Cell 94, 739–750 (1998).

    CAS  PubMed  Google Scholar 

  46. Cecconi, F., Alvarez-Bolado, G., Meyer, B.I., Roth, K.A. & Gruss, P. Apaf1 (CED-4 homolog) regulates programmed cell death in mammalian development. Cell 94, 727–737 (1998).

    CAS  PubMed  Google Scholar 

  47. Soengas, M.S. et al. Apaf-1 and caspase-9 in p53-dependent apoptosis and tumor inhibition. Science 284, 156–159 (1999).

    CAS  PubMed  Google Scholar 

  48. Fearnhead, H.O. et al. Oncegene-dependent apoptosis is mediated by caspase-9. Proc. Natl. Acad. Sci. USA 95, 13664–13669 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Soengas, M.S. et al. Inactivation of the apoptosis effector Apaf-1 in malignant melanoma. Nature 409, 207–211 (2001).

    CAS  PubMed  Google Scholar 

  50. Hofmann, K. & Bucher, P. The CARD domain: a new apoptotic signaling motif. Trends. Biochem. Sci. 22, 155–156 (1997).

    CAS  PubMed  Google Scholar 

  51. Chou, J.J., Matsuo, H., Duan, H. & Wagner, G. Solution structure of the RAIDD CARD and model for CARD/CARD interaction in caspase-2 and caspase-9 recruitment. Cell 94, 171–180 (1998).

    CAS  PubMed  Google Scholar 

  52. Qin, H. et al. Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1. Nature 399, 547–555 (1999).

    Google Scholar 

  53. Zhou, P., Chou, J., Olea, R.S., Yuan, J. & Wagner, G. Solution structure of Apaf-1 CARD and its interaction with caspase-9 CARD: a structural basis for specific adaptor/caspase interaction. Proc. Natl. Acad. Sci. USA 96, 11265–11270 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Vaughn, D.E., Rodriguez, J., Lazebnik, Y. & Joshua-Tor, L. Crystal structure of Apaf-1 caspase recruitment domain: an alpha-helical Greek key fold for apoptotic signaling. J. Mol. Biol. 293, 439–447 (1999).

    CAS  PubMed  Google Scholar 

  55. Day, C.L., Dupont, C., Lackmann, M., Vaux, D.L. & Hinds, M.G. Solution structure and mutagenesis of the caspase recruitment domain (CARD) from Apaf-1. Cell Death Differ. 6, 1125–1132 (1999).

    CAS  PubMed  Google Scholar 

  56. Huang, B., Eberstadt, M., Olejniczak, E.T., Meadows, R.P. & Fesik, S.W. NMR structure and mutagenesis of the Fas (APO-1/CD95) death domain. Nature 384, 638–641 (1996).

    CAS  PubMed  Google Scholar 

  57. liepinsh, E., Ilag, L.L., Otting, G. & Ibanez, C.F. NMR structure of the death domain of the p75 neurotrophin receptor. EMBO J. 16, 4999–5005 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Jeong, E.-J. et al. The solution structure of FADD death domain. J. Biol. Chem. 274, 16337–16342 (1999).

    CAS  PubMed  Google Scholar 

  59. Xiao, T., Towb, P., Wasserman, S.A. & Sprang, S.R. Three-dimensional structure of a complex between the death domains of Pelle and Tube. Cell 99, 545–555 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Eberstadt, M. et al. NMR structure and mutagenesis of the FADD (Mort1) death-effector domain. Nature 392, 941–945 (1998).

    CAS  PubMed  Google Scholar 

  61. Tamm, I. et al. Expression and prognostic significance of IAP-family genes in human cancers and myeloid leukemias. Clin. Cancer Res. 6, 1796–1803 (2000).

    CAS  PubMed  Google Scholar 

  62. LaCasse, E.C., Baird, S., Korneluk, R.G. & MacKenzie, A.E. The inhibitor of apoptosis (IAPs) and their emerging role in cancer. Oncogene 17, 3247–3259 (1998).

    PubMed  Google Scholar 

  63. Ambrosini, G., Adida, C. & Altieri, D.C. A novel anti-apoptosis gene, survivin, expressed in cancer and lymphoma. Nature Med. 3, 917–921 (1997).

    CAS  PubMed  Google Scholar 

  64. Liu, Z. et al. Structural basis for binding of Smac/DIABLO to the XIAP BIR3 domain. Nature 408, 1004–1008 (2000).

    CAS  PubMed  Google Scholar 

  65. Wu, G. et al. Structural basis of IAP recognition by Smac/DIABLO. Nature 408, 1008–1012 (2000).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  67. Datta, R. et al. XIAP regulates DNA damage-induced apoptosis downstream of caspase-9 cleavage. J. Biol. Chem. 275, 31733–31738 (2000).

    CAS  PubMed  Google Scholar 

  68. Wei, Y. et al. The structures of caspases-1, -3, -7 and -8 reveal the basis for substrate and inhibitor selectivity. Chem. Biol. 7, 423–432 (2000).

    CAS  PubMed  Google Scholar 

  69. Hozak, R.R., Manji, G.A. & Friesen, P.D. The BIR motifs mediate dominant interference and oligomerization of inhibitor of apoptosis Op-IAP. Mol. Cell. Biol. 20, 1877–1885 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Chai, J. et al. Structural basis of caspase-7 inhibiton by XIAP. Cell 104, 769–780 (2001).

    CAS  PubMed  Google Scholar 

  71. Huang, Y. et al. Structural basis of caspase inhibition by XIAP: differential roles of the linker versus the BIR domain. Cell 104, 781–790 (2001).

    CAS  PubMed  Google Scholar 

  72. Riedl, S.J. et al. Structural basis for the inhibition of caspase-3 by XIAP. Cell 104, 791–800 (2001).

    CAS  PubMed  Google Scholar 

  73. Bump, N.J. et al. Inhibition of ICE family proteases by baculovirus antiapoptotic protein p35. Science 269, 1885–1888 (1995).

    CAS  PubMed  Google Scholar 

  74. Zhou, Q. et al. Interaction of the baculovirus anti-apoptotic protein p35 with caspases. Specificity, kinetics, and characterization of the caspase/p35 complex. Biochemistry 37, 10757–10765 (1998).

    CAS  PubMed  Google Scholar 

  75. Xu, G. et al. Covalent inhibition revealed by the crystal structure of the caspase-8/p35 complex. Nature 410, 494–497 (2001).

    CAS  PubMed  Google Scholar 

  76. Gross, A., McDonnell, J.M. & Korsmeyer, S.J. BCL-2 family members and the mitochondria in apoptosis. Genes Dev. 13, 1899–1911 (1999).

    CAS  PubMed  Google Scholar 

  77. Vander Heiden, M.G. & Thompson, C.B. Bcl-2 proteins: regulators of apoptosis or of mitochondrial homeostasis. Nature Cell Biol. 1, E209–E216 (1999).

    CAS  PubMed  Google Scholar 

  78. Korsmeyer, S.J. et al. Pro-apoptotic cascade activates BID, which oligomerizes BAK or BAX into pores that result in the release of cytochrome c. Cell Death Differ. 7, 1166–1173 (2000).

    CAS  PubMed  Google Scholar 

  79. Antonsson, B., Montessuit, S., Lauper, S., Eskes, R. & Martinou, J.-C. Bax oligomerization is required for channel-forming activity in liposomes and to trigger cytochrome c release from mitochondria. Biochem. J. 345, 271–278 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Yu, J., Zhang, L., Hwang, P.M., Kinzler, K.W. & Vogelstein, B. PUMA induces the rapid apoptosis of colorectal cancer cells. Mol. Cell 7, 673–682 (2001).

    CAS  PubMed  Google Scholar 

  81. Li, K. et al. Cytochrome c deficiency causes embryonic lethality and attenuates stress-induced apoptosis. Cell 101, 389–399 (2000).

    CAS  PubMed  Google Scholar 

  82. Igaki, T. et al. Drob1, a Drosophila member of the Bcl-2/CED-9 family that promotes cell death. Proc. Natl. Acad. Sci. USA 97, 662–667 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Brachmann, C.B., Jassim, O.W., Wachsmuth, B.D. & Cagan, R.L. The Drosophila Bcl-2 family member dBorg-1 functions in the apoptotic response to UV-irradiation. Curr. Biol. 10, 547–550 (2000).

    CAS  PubMed  Google Scholar 

  84. Colussi, P.A. et al. Debcl, a aroapoptotic Bcl-2 homologue, is a component of the Drosophila melanogaster cell death machinery. J. Cell Biol. 148, 703–714 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Zhang, H. et al. Drosophila Pro-apoptotic Bcl-2/Bax homologue reveals evolutionary conservation of dell death mechanisms. J. Biol. Chem. 275, 27303–27306 (2000).

    CAS  PubMed  Google Scholar 

  86. Levine, A.J. p53, the cellular gatekeeper for growth and division. Cell 88, 323–331 (1997).

    CAS  PubMed  Google Scholar 

  87. Yang, Y., Fang, S., Jensen, J.P., Weissman, A.M. & Ashwell, J.D. Ubiquitin protein ligase activity of IAPs and their degradation in proteasomes in response to apoptotic stimuli. Science 288, 874–877 (2000).

    CAS  PubMed  Google Scholar 

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Acknowledgements

The author thanks B. Hay, D. Xue, and F. Hughson for critically reading the manuscript, members of the Shi laboratory for discussions, N. Hunt for secretarial assistance, and H. Wu and B. Vogelstein for sharing manuscripts before publication. The author wishes to apologize to those colleagues whose work is not cited here due to space limitations.

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Shi, Y. A structural view of mitochondria-mediated apoptosis. Nat Struct Mol Biol 8, 394–401 (2001). https://doi.org/10.1038/87548

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