Apoptosome Structure, Assembly, and Procaspase Activation
2013; Elsevier BV; Volume: 21; Issue: 4 Linguagem: Inglês
10.1016/j.str.2013.02.024
ISSN1878-4186
AutoresShujun Yuan, Christopher W. Akey,
Tópico(s)Phagocytosis and Immune Regulation
ResumoApaf-1-like molecules assemble into a ring-like platform known as the apoptosome. This cell death platform then activates procaspases in the intrinsic cell death pathway. In this review, crystal structures of Apaf-1 monomers and CED-4 dimers have been combined with apoptosome structures to provide insights into the assembly of cell death platforms in humans, nematodes, and flies. In humans, the caspase recognition domains (CARDs) of procaspase-9 and Apaf-1 interact with each other to form a CARD-CARD disk, which interacts with the platform to create an asymmetric proteolysis machine. The disk tethers multiple pc-9 catalytic domains to the platform to raise their local concentration, and this leads to zymogen activation. These findings have now set the stage for further studies of this critical activation process on the apoptosome. Apaf-1-like molecules assemble into a ring-like platform known as the apoptosome. This cell death platform then activates procaspases in the intrinsic cell death pathway. In this review, crystal structures of Apaf-1 monomers and CED-4 dimers have been combined with apoptosome structures to provide insights into the assembly of cell death platforms in humans, nematodes, and flies. In humans, the caspase recognition domains (CARDs) of procaspase-9 and Apaf-1 interact with each other to form a CARD-CARD disk, which interacts with the platform to create an asymmetric proteolysis machine. The disk tethers multiple pc-9 catalytic domains to the platform to raise their local concentration, and this leads to zymogen activation. These findings have now set the stage for further studies of this critical activation process on the apoptosome. Apoptotic protease activation factor-1 resides in the cytoplasm of healthy cells as an inactive monomer (Liu et al., 1996Liu X. Kim C.N. Yang J. Jemmerson R. Wang X. 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The CED-4 apoptosome binds and activates CED-3, the only procaspase in nematodes, in a step mediated by homotypic interactions between caspase recognition domains (CARDs) located at the N termini of CED-3 and CED-4 (Yang et al., 1998Yang X. Chang H.Y. Baltimore D. Essential role of CED-4 oligomerization in CED-3 activation and apoptosis.Science. 1998; 281: 1355-1357Crossref PubMed Scopus (235) Google Scholar; Seshagiri and Miller, 1997Seshagiri S. Miller L.K. Caenorhabditis elegans CED-4 stimulates CED-3 processing and CED-3-induced apoptosis.Curr. Biol. 1997; 7: 455-460Abstract Full Text Full Text PDF PubMed Google Scholar). Intriguingly, CED-3 without the N-terminal CARD was reported to bind to the underside of the CED-4 apoptosome, resulting in a 5- to 10-fold increase in the proteolytic activity of CED-3 (Qi et al., 2010Qi S. Pang Y. Hu Q. Liu Q. Li H. Zhou Y. He T. Liang Q. Liu Y. Yuan X. et al.Crystal structure of the Caenorhabditis elegans apoptosome reveals an octameric assembly of CED-4.Cell. 2010; 141: 446-457Abstract Full Text Full Text PDF PubMed Scopus (137) Google Scholar). However, the relevance of this observation is not clear given the absence of bona fide CARD-CARD interactions between the procaspase and CED-4. In humans, cytochrome c is released from binding sites on the inner mitochondrial membrane that contain cardiolipin molecules (reviewed in Gonzalvez and Gottlieb, 2007Gonzalvez F. Gottlieb E. Cardiolipin: setting the beat of apoptosis.Apoptosis. 2007; 12: 877-885Crossref PubMed Scopus (238) Google Scholar). In response to the appropriate signals, proapoptotic Bcl-2 family members are thought to form pores in the outer mitochrondrial membrane through which cytochrome c and other protein effectors flow into the cytoplasm (reviewed in Brunelle and Letai, 2009Brunelle J.K. Letai A. Control of mitochondrial apoptosis by the Bcl-2 family.J. 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Cell Biol. 2004; 5: 897-907Crossref PubMed Scopus (1567) Google Scholar). Inhibitors of apoptosis (IAPs), such as XIAP, are modular proteins that contain ∼70 residue Baculovirus IAP Repeat (BIR) domains that inhibit procaspases. In XIAP, the BIR3 domain interacts with the clipped p20-p10 linker of processed pc-9 (Shiozaki et al., 2003Shiozaki E.N. Chai J. Rigotti D.J. Riedl S.J. Li P. Srinivasula S.M. Alnemri E.S. Fairman R. Shi Y. Mechanism of XIAP-mediated inhibition of caspase-9.Mol. Cell. 2003; 11: 519-527Abstract Full Text Full Text PDF PubMed Scopus (573) Google Scholar), whereas the linker between BIR1 and BIR2 interacts with the active site of caspase-3 (Riedl et al., 2001Riedl S.J. Renatus M. Schwarzenbacher R. Zhou Q. Sun C. Fesik S.W. Liddington R.C. Salvesen G.S. Structural basis for the inhibition of caspase-3 by XIAP.Cell. 2001; 104: 791-800Abstract Full Text Full Text PDF PubMed Scopus (656) Google Scholar, Fesik and Shi, 2001Fesik S.W. Shi Y. Structural biology. 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Zou H. Chen P. Wang X. Abrams J.M. Dark is a Drosophila homologue of Apaf-1/CED-4 and functions in an evolutionarily conserved death pathway.Nat. Cell Biol. 1999; 1: 272-279Crossref PubMed Scopus (293) Google Scholar; Zhou et al., 1999Zhou 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. 1999; 4: 745-755Abstract Full Text Full Text PDF PubMed Scopus (181) Google Scholar; Kanuka et al., 1999Kanuka H. Sawamoto K. Inohara N. Matsuno K. Okano H. Miura M. Control of the cell death pathway by Dapaf-1 a Drosophila Apaf-1/CED-4 related caspase activator.Mol. Cell. 1999; 4: 757-769Abstract Full Text Full Text PDF PubMed Scopus (213) Google Scholar) assembles into an octameric apoptosome (Yu et al., 2006Yu 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. 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Finally, the activation of initiator procaspases is discussed in light of recent structures of pc-9 apoptosomes that revealed an asymmetric proteolysis machine (Yuan et al., 2011bYuan S. Yu X. Asara J.M. Heuser J.E. Ludtke S.J. Akey C.W. The holo-apoptosome: activation of procaspase-9 and interactions with procaspase-3.Structure. 2011; 19: 1084-1096Abstract Full Text Full Text PDF PubMed Scopus (64) Google Scholar). In a unifying proposal, we suggest that initiator procaspases may be activated in a conserved manner in all metazoans. Thus, a CARD-CARD disk in the holo-apoptosome may tether catalytic domains in close proximity to the platform and regulate the accessibility of platform binding sites that mediate procaspase activation (Yuan et al., 2010Yuan S. Yu X. Topf M. Ludtke S.J. Wang X. Akey C.W. Structure of an apoptosome-procaspase-9 CARD complex.Structure. 2010; 18: 571-583Abstract Full Text Full Text PDF PubMed Scopus (108) Google Scholar, Yuan et al., 2011bYuan S. Yu X. 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These proteins contain three tandemly arrayed domains within the nucleotide-binding and oligomerization domain (NOD; Figure 2A). The nucleotide-binding domain (NBD) and helix domain 1 (HD1) create a binding pocket for ATP and ADP (or their deoxy analogs). These domains are predicted to oligomerize and form a ring, based on their roles in other AAA+ ATPases (Riedl et al., 2005Riedl S.J. Li W. Chao Y. Schwarzenbacher R. Shi Y. Structure of the apoptotic protease-activating factor 1 bound to ADP.Nature. 2005; 434: 926-933Crossref PubMed Scopus (280) Google Scholar; Diemand and Lupas, 2006Diemand A.V. Lupas A.N. Modeling AAA+ ring complexes from monomeric structures.J. Struct. Biol. 2006; 156: 230-243Crossref PubMed Scopus (54) Google Scholar; Danot et al., 2009Danot O. Marquenet E. Vidal-Ingigliardi D. Richet E. Wheel of life, wheel of death: a mechanistic insight into signaling by STAND proteins.Structure. 2009; 17: 172-182Abstract Full Text Full Text PDF PubMed Scopus (126) Google Scholar). A novel winged helix domain (WHD) follows HD1 and also participates in ring formation (Qi et al., 2010Qi S. Pang Y. Hu Q. Liu Q. Li H. Zhou Y. He T. Liang Q. Liu Y. Yuan X. et al.Crystal structure of the Caenorhabditis elegans apoptosome reveals an octameric assembly of CED-4.Cell. 2010; 141: 446-457Abstract Full Text Full Text PDF PubMed Scopus (137) Google Scholar; Yuan et al., 2010Yuan S. Yu X. Topf M. Ludtke S.J. Wang X. Akey C.W. Structure of an apoptosome-procaspase-9 CARD complex.Structure. 2010; 18: 571-583Abstract Full Text Full Text PDF PubMed Scopus (108) Google Scholar, Yuan et al., 2011bYuan S. Yu X. Asara J.M. Heuser J.E. Ludtke S.J. Akey C.W. The holo-apoptosome: activation of procaspase-9 and interactions with procaspase-3.Structure. 2011; 19: 1084-1096Abstract Full Text Full Text PDF PubMed Scopus (64) Google Scholar). A moderately conserved helical domain, denoted HD2, is located after the NOD and forms an arm that extends from the central hub to support two β-propellers in human and fly apoptosomes (Figures 1 and 2A; Yuan et al., 2010Yuan S. Yu X. Topf M. Ludtke S.J. Wang X. Akey C.W. Structure of an apoptosome-procaspase-9 CARD complex.Structure. 2010; 18: 571-583Abstract Full Text Full Text PDF PubMed Scopus (108) Google Scholar, Yuan et al., 2011aYuan S. Yu X. Topf M. Dorstyn L. Kumar S. Ludtke S.J. Akey C.W. Structure of the Drosophila apoptosome at 6.9Å resolution.Structure. 2011; 19: 128-140Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar; Yu et al., 2005Yu X. Acehan D. Menetret J.F. Booth C.R. Ludtke S.J. Riedl S.J. Shi Y. Wang X. Akey C.W. A structure of the human apoptosome at 12.8 Å resolution provides insights into this cell death platform.Structure. 2005; 13: 1725-1735Abstract Full Text Full Text PDF PubMed Scopus (122) Google Scholar, Yu et al., 2006Yu 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. 2006; 355: 577-589Crossref PubMed Scopus (114) Google Scholar). The N-terminal effector domain in Apaf-1 like proteins is a CARD that mediates homotypic interactions with a procaspase CARD. In total, there are 23 NOD proteins in humans, but only Apaf-1 facilitates apoptosis. Other NOD proteins are predicted to form signaling or activation platforms in inflammation pathways (Proell et al., 2008Proell M. Riedl S.J. Fritz J.H. Rojas A.M. Schwarzenbacher R. 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Structure of an apoptosome-procaspase-9 CARD complex.Structure. 2010; 18: 571-583Abstract Full Text Full Text PDF PubMed Scopus (108) Google Scholar, Yuan et al., 2011aYuan S. Yu X. Topf M. Dorstyn L. Kumar S. Ludtke S.J. Akey C.W. Structure of the Drosophila apoptosome at 6.9Å resolution.Structure. 2011; 19: 128-140Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar; Reubold et al., 2011Reubold T.F. Wohlgemuth S. Eschenburg S. Crystal structure of full-length apaf-1: how the death signal is relayed in the mitochondrial pathway of apoptosis.Structure. 2011; 19: 1074-1083Abstract Full Text Full Text PDF PubMed Scopus (87) Google Scholar). Truncation of CED-4 reflects a different strategy for regulating apoptosome assembly in worms, wherein CED-9 forms a complex with a CED-4 lateral dimer to prevent further assembly (Yan et al., 2004Yan N. Wu J.W. Chai J. Li W. Shi Y. Molecular mechanisms of DrICE inhibition by DIAP1 and removal of inhibition by Reaper, Hid and Grim.Nat. Struct. Mol. Biol. 2004; 11: 420-428Crossref PubMed Scopus (87) Google Scholar, Yan et al., 2005Yan N. Chai J. Lee E.S. Gu L. Liu Q. He J. Wu J.W. Kokel D. Li H. Hao Q. et al.Structure of the CED-4-CED-9 complex provides insights into programmed cell death in Caenorhabditis elegans.Nature. 2005; 437: 831-837Crossref PubMed Scopus (178) Google Scholar; Figures 1 and 2B). In the lateral dimer, both CED-4 monomers bind ATP and adopt an extended conformation, whereas CED-9 blocks the NBD in monomer A to prevent ring formation. Intriguingly, the N-terminal CARD of CED-4 sits atop the NBD in monomer A, whereas the CARD in monomer B is completely disordered in the crystal. Hence, both CARDs in the CED-4 lateral dimer appear be accessibl
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