Caspase-9, Bcl-XL, and Apaf-1 Form a Ternary Complex

Genetic analysis of apoptosis in the nematodeCaenorhabditis elegans has revealed the cell death machine to be composed of three core interacting components. CED-4 (equivalent to mammalian Apaf-1) is a nucleotide binding molecule that complexes with the zymogen form of the death protease CED-3, leading to its autoactivation and cell death. CED-9 blocks death by complexing with CED-4 and attenuating its ability to promote CED-3 activation. An equivalent ternary complex was found to be present in mammalian cells involving Apaf-1, the mammalian death protease caspase-9, and Bcl-XL, an anti-apoptotic member of the Bcl-2 family. Consistent with a central role for caspase-9, a dominant negative form effectively inhibited cell death initiated by a wide variety of inducers. Genetic analysis of apoptosis in the nematodeCaenorhabditis elegans has revealed the cell death machine to be composed of three core interacting components. CED-4 (equivalent to mammalian Apaf-1) is a nucleotide binding molecule that complexes with the zymogen form of the death protease CED-3, leading to its autoactivation and cell death. CED-9 blocks death by complexing with CED-4 and attenuating its ability to promote CED-3 activation. An equivalent ternary complex was found to be present in mammalian cells involving Apaf-1, the mammalian death protease caspase-9, and Bcl-XL, an anti-apoptotic member of the Bcl-2 family. Consistent with a central role for caspase-9, a dominant negative form effectively inhibited cell death initiated by a wide variety of inducers. Programmed cell death, or apoptosis, is an evolutionarily conserved and genetically regulated biological process that plays an important role in the development and homeostasis of multicellular organisms (1Nagata S. Cell. 1997; 88: 355-365Abstract Full Text Full Text PDF PubMed Scopus (4559) Google Scholar, 2Steller H. 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Biol. 1996; 6: 555-562Abstract Full Text Full Text PDF PubMed Google Scholar). Caspases exist as zymogens composed of a prodomain plus large and small catalytic subunits. Generation of the active enzyme requires accurate processing at internal Asp residues to liberate the prodomain and produce the two chain active enzyme (7Takahashi A. Earnshaw W.C. Curr. Opin. Genet. Dev. 1996; 6: 50-55Crossref PubMed Scopus (151) Google Scholar, 8Chinnaiyan A.C. Dixit V.M. Curr. Biol. 1996; 6: 555-562Abstract Full Text Full Text PDF PubMed Google Scholar, 9Chinnaiyan A.C. Dixit V.M. Semin. Immunol. 1997; 9: 69-76Crossref PubMed Scopus (94) Google Scholar). Caspases can be classified according to whether they possess a large or a small prodomain. Large prodomains function as signal integrators as they bind adapter molecules involved in signal transduction. For example, the death effector domain within the prodomain of caspase-8 binds to the corresponding motif in the adapter molecule FADD 1The abbreviations used are: FADD, Fas-associated death domain; RAIDD, RIP-associated ICH-1/CED-3-homologous protein with a death domain; TRADD, tumor necrosis factor-associated death domain. TNF, tumor necrosis factor; mAb, monoclonal antibody. allowing for its recruitment to the CD-95 death receptor signaling complex (10Fraser A. Evan G. Cell. 1996; 85: 781-784Abstract Full Text Full Text PDF PubMed Scopus (613) Google Scholar, 11Chinnaiyan A.M. O'Rourke K. Tewari M. Dixit V.M. Cell. 1995; 81: 505-512Abstract Full Text PDF PubMed Scopus (2161) Google Scholar). The death effector domain is a specific example of a more global homophilic interaction domain termed CARD (for caspaserecruitment domain) that is present in other large prodomains including those of caspase-2 (ICH-1) and caspase-9 (ICE-LAP6, Mch6; Ref. 12Hofmann K. Bucher P. Tschopp J. Trends Biochem. Sci. 1997; 22: 155-156Abstract Full Text PDF PubMed Scopus (448) Google Scholar). Caspase-2 is recruited to the TNFR-1 signaling complex through an interaction involving the respective CARD domains within the adapter molecule RAIDD and the prodomain of caspase-2 (13Duan H. Dixit V.M. Nature. 1997; 385: 86-89Crossref PubMed Scopus (469) Google Scholar). To date, the other large prodomain-containing caspase, caspase-9, has not been implicated in any specific signaling pathway (14Duan H. Orth K. Chinnaiyan A.C. Poirier G.G. Froelich C.J. He W. Dixit V.M. J. Biol. Chem. 1996; 271: 16720-16724Abstract Full Text Full Text PDF PubMed Scopus (297) Google Scholar). We find that caspase-9 is part of a ternary signaling complex analogous to the one present in C. elegans involving CED-3, CED-4, and CED-9 (6Golstein P. Science. 1997; 275: 1081-1082Crossref PubMed Scopus (336) Google Scholar, 15Chinnaiyan A.M. O'Rourke K. Lane B.R. Dixit V.M. Science. 1997; 275: 1122-1126Crossref PubMed Scopus (554) Google Scholar, 16Wu D. Wallen H.D. Nunez G. Science. 1997; 275: 1126-1129Crossref PubMed Scopus (285) Google Scholar, 17Spector M.S. Desnoyers S. Hoeppner D.J. Hengatner M.O. Nature. 1997; 385: 653-656Crossref PubMed Scopus (256) Google Scholar). CED-9 is an inhibitor of apoptosis in the nematode and corresponds to mammalian cell death inhibitors including Bcl-2 and Bcl-XL (18Hengartner M.O. Horvitz H.R. Cell. 1994; 76: 665-676Abstract Full Text PDF PubMed Scopus (1046) Google Scholar). It can be found complexed with the nematode caspase equivalent CED-3 in the presence of the bridging molecule CED-4 (15Chinnaiyan A.M. O'Rourke K. Lane B.R. Dixit V.M. Science. 1997; 275: 1122-1126Crossref PubMed Scopus (554) Google Scholar, 16Wu D. Wallen H.D. Nunez G. Science. 1997; 275: 1126-1129Crossref PubMed Scopus (285) Google Scholar, 17Spector M.S. Desnoyers S. Hoeppner D.J. Hengatner M.O. Nature. 1997; 385: 653-656Crossref PubMed Scopus (256) Google Scholar). This suggests that a molecular mechanism based on the physical interaction of these components could potentially account for the inhibitory function of CED-9 and, by extension, Bcl-XL and Bcl-2 (5Hengartner M.O. Curr. Opin. Genet. Dev. 1996; 6: 34-38Crossref PubMed Scopus (91) Google Scholar). The ability of the worm genes to function in mammalian cells underscores their conservation and the interchangeability of key death components (15Chinnaiyan A.M. O'Rourke K. Lane B.R. Dixit V.M. Science. 1997; 275: 1122-1126Crossref PubMed Scopus (554) Google Scholar, 16Wu D. Wallen H.D. Nunez G. Science. 1997; 275: 1126-1129Crossref PubMed Scopus (285) Google Scholar). For example, in transfected human embryonic kidney cells, CED-4 bound CED-9 or its mammalian counterpart Bcl-XL. Similarly, CED-4 bound CED-3 or corresponding large prodomain mammalian caspases (including caspase-1 and caspase-8) but not small prodomain caspases like caspase-3. The inability of dominant negative versions of caspase-1 or caspase-8 to block CED-4-induced cell death suggested that either another distinct large prodomain caspase was the primary target or that CED-4 activated multiple caspases (15Chinnaiyan A.M. O'Rourke K. Lane B.R. Dixit V.M. Science. 1997; 275: 1122-1126Crossref PubMed Scopus (554) Google Scholar). The exact mechanism deployed by CED-4 to activate CED-3 and/or caspases remains unclear. It has been shown, however, that CED-4 is a P-loop-containing nucleotide binding protein that is capable of promoting the activation of CED-3 and that this is blocked by CED-9 (19Chinnaiyan A.M. Chaudhary D. O'Rourke K. Dixit V.M. Nature. 1997; 388: 728-729Crossref PubMed Scopus (164) Google Scholar, 20James C. Gschmeissner S. Fraser A. Evan G.I. Curr. Biol. 1997; 7: 246-252Abstract Full Text Full Text PDF PubMed Scopus (122) Google Scholar, 21Seshagiri S. Miller L.K. Curr. Biol. 1997; 7: 455-460Abstract Full Text Full Text PDF PubMed Google Scholar). Recently, a human CED-4 homologue (Apaf-1) has been identified that possesses an NH2-terminal CED-3 prodomain-like region that includes a CARD domain, a CED-4-like segment including conserved P-loop and a COOH-terminal extension composed of multiple WD-40 repeats that are lacking in nematode CED-4 (Fig. 1 A; Ref. 22Zou H. Henzel W.J. Liu X. Lutschg A. Wang X. Cell. 1997; 90: 405-413Abstract Full Text Full Text PDF PubMed Scopus (2743) Google Scholar). Apaf-1, in the presence of cytochrome c, nucleotide (dATP), and a previously unidentified factor (Apaf-3) that has recently been shown to be caspase 9 (31Li P. Nijhawan D. Budhihardjo I. Srinivasula S. Ahmad M. Alnemri E. Wang W. Cell. 1997; 91: 479-489Abstract Full Text Full Text PDF PubMed Scopus (6239) Google Scholar), is able to promote the activation of caspase-3 (a small prodomain downstream caspase) by a mechanism that awaits definition (23Liu X. Kim C.N. Yang J. Jemmerson R. Wang X. Cell. 1996; 86: 147-157Abstract Full Text Full Text PDF PubMed Scopus (4463) Google Scholar, 24Vaux D.L. Cell. 1997; 90: 389-390Abstract Full Text Full Text PDF PubMed Scopus (103) Google Scholar, 25Jacobson M.D. Curr. Biol. 1997; 7: R277-R281Abstract Full Text Full Text PDF PubMed Google Scholar). We found that caspase-9, but not other large prodomain caspases, and Bcl-XL bound distinct regions in Apaf-1 and that dominant negative caspase-9 effectively blocked cell death induced by a variety of effectors. Thus, caspase-9 likely represents a direct downstream target of Apaf-1 and its activation appears critical for the propagation of death signals. cDNAs encoding Apaf-1 or its truncated forms were obtained by polymerase chain reaction based on the published Apaf-1 DNA sequence (22Zou H. Henzel W.J. Liu X. Lutschg A. Wang X. Cell. 1997; 90: 405-413Abstract Full Text Full Text PDF PubMed Scopus (2743) Google Scholar). The full-length Apaf-1 was cloned into pcDNA3 (Invitrogen) with a NH2-terminal Flag tag. Apaf-1(3+4)-Myc (amino acids 1–412), Apaf-1(3)-Myc (amino acids 1–102), and Apaf-1(4)-Myc (amino acids 86–412) were cloned into pcDNA3.1(−)/Myc-His B (Invitrogen) with a COOH-terminal Myc tag provided by the vector. The construct expressing caspase-9-prodomain (amino acids 1–168) was cloned by polymerase chain reaction into pcDNA3 with a COOH-terminal Flag tag. The constructs encoding HA-BAX, HA-BAK, HA-BIK, Bcl-XL-Myc, Bcl-XL-Flag, Bcl-XLmt1-Flag, Bcl-XLmt7-Flag, caspase-1-Flag, caspase-2-prodomain-Flag, caspase-3-Flag, caspase-8-DN-Flag, caspase-9-DN-Flag, caspase-9 p30-Flag (amino acids 130–416), CED-4-Myc, FADD, RAIDD, TRADD-Myc, cIAP1, and CrmA have been described elsewhere (11Chinnaiyan A.M. O'Rourke K. Tewari M. Dixit V.M. Cell. 1995; 81: 505-512Abstract Full Text PDF PubMed Scopus (2161) Google Scholar, 13Duan H. Dixit V.M. Nature. 1997; 385: 86-89Crossref PubMed Scopus (469) Google Scholar, 14Duan H. Orth K. Chinnaiyan A.C. Poirier G.G. Froelich C.J. He W. Dixit V.M. J. Biol. Chem. 1996; 271: 16720-16724Abstract Full Text Full Text PDF PubMed Scopus (297) Google Scholar, 15Chinnaiyan A.M. O'Rourke K. Lane B.R. Dixit V.M. Science. 1997; 275: 1122-1126Crossref PubMed Scopus (554) Google Scholar, 26Chinnaiyan A.M. O'Rourke K. Yu G.-L. Lyons R.H. Garg M. Duan R.D. Xing L. Gentz R. Ni J. Dixit V.M. Science. 1996; 274: 990-992Crossref PubMed Scopus (531) Google Scholar). Cell death assays were performed as described (26Chinnaiyan A.M. O'Rourke K. Yu G.-L. Lyons R.H. Garg M. Duan R.D. Xing L. Gentz R. Ni J. Dixit V.M. Science. 1996; 274: 990-992Crossref PubMed Scopus (531) Google Scholar, 27Pan G. O'Rourke K. Chinnaiyan A.M. Gentz R. Ebner R. Ni J. Dixit V.M. Science. 1997; 276: 111-113Crossref PubMed Scopus (1561) Google Scholar). MCF7 cells were transfected using the lipofectAMINE procedure (Life Technologies, Inc.) according to the manufacturer's instructions. in vivo interaction assays have been described elsewhere (26Chinnaiyan A.M. O'Rourke K. Yu G.-L. Lyons R.H. Garg M. Duan R.D. Xing L. Gentz R. Ni J. Dixit V.M. Science. 1996; 274: 990-992Crossref PubMed Scopus (531) Google Scholar, 28Pan G. Ni J. Wei Y.-F. Yu G.-L. Gentz R. Dixit V.M. Science. 1997; 277: 815-818Crossref PubMed Scopus (1381) Google Scholar). 293 cells were transfected by means of calcium phosphate precipitation. As shown in Fig. 1 B, dominant negative caspase-9 (caspase-9-DN) inhibited cell death induced by the receptor associated death adapter molecules FADD and TRADD in human breast carcinoma MCF7 cells, consistent with caspase-9 functioning downstream of these two adapter molecules. Importantly, CED-4-induced apoptosis, which had previously been shown not to be blocked by dominant negative forms of the other large prodomain caspases (including caspase-2 and caspase-8) (9Chinnaiyan A.C. Dixit V.M. Semin. Immunol. 1997; 9: 69-76Crossref PubMed Scopus (94) Google Scholar), was blocked by dominant negative caspase-9. It is therefore probable that nematode CED-4 induces apoptosis in mammalian cells by activating caspase-9. In keeping with this observation, we have previously noted that caspase-9 physically interacts with CED-4 (14Duan H. Orth K. Chinnaiyan A.C. Poirier G.G. Froelich C.J. He W. Dixit V.M. J. Biol. Chem. 1996; 271: 16720-16724Abstract Full Text Full Text PDF PubMed Scopus (297) Google Scholar). To determine if caspase-9 similarly bound the mammalian CED-4 equivalent Apaf-1, co-immunoprecipitation was undertaken in human embryonic kidney 293 cells. Flag-Apaf-1 was found to co-precipitate with caspase-9 (Fig. 2 A). Since caspase-9-DN-Flag also bound truncated Apaf-1 (Apaf-1(3+4); residues 1–412) that contained only the CED-3 and CED-4 homologous regions (Fig. 2 B, left), further analysis used only this truncated form. Caspase-9-DN-Flag, but not other large prodomain-containing caspases, specifically immunoprecipitated with Apaf-1 (Fig. 2 B, left). Therefore, unlike CED-4, which appears to promiscuously bind large prodomain caspases, Apaf-1 was specific for caspase-9. Additionally, as expected, the small prodomain-containing caspase-3 did not bind Apaf-1. The specificity of this interaction was confirmed by the finding that caspase-2, a CARD-containing large prodomain caspase, bound its cognate adapter molecule RAIDD through a CARD-mediated interaction, yet did not interact with the Apaf-1 CARD domain (Fig. 2 B, right). To delineate the Apaf-1 interacting domain in caspase-9, both a prodomainless form (caspase-9 p30-Flag) and a prodomain only expressing form were assessed in binding studies. Consistent with the expected involvement of the prodomain in recruitment to signaling complexes, only the prodomain of caspase-9 was required to interact with Apaf-1(3+4)-Myc (Fig. 2 C). Given that CED-9 binds CED-4 (15Chinnaiyan A.M. O'Rourke K. Lane B.R. Dixit V.M. Science. 1997; 275: 1122-1126Crossref PubMed Scopus (554) Google Scholar, 16Wu D. Wallen H.D. Nunez G. Science. 1997; 275: 1126-1129Crossref PubMed Scopus (285) Google Scholar, 17Spector M.S. Desnoyers S. Hoeppner D.J. Hengatner M.O. Nature. 1997; 385: 653-656Crossref PubMed Scopus (256) Google Scholar), we asked whether an equivalent interaction existed between the corresponding mammalian counterparts Bcl-XL and Apaf-1. Upon co-transfection, Flag-Apaf-1 co-precipitated with Bcl-XL-Myc (Fig. 2 A). We consistently observed that Apaf-1 expression was enhanced by co-expressing Bcl-XL (15Chinnaiyan A.M. O'Rourke K. Lane B.R. Dixit V.M. Science. 1997; 275: 1122-1126Crossref PubMed Scopus (554) Google Scholar), suggesting that Bcl-XL may stabilize Apaf-1. Bcl-XL-Flag also co-immunoprecipitated with Apaf-1(3+4)-Myc as well as CED-4-Myc (Fig. 2 D, left and middle). Previous studies had shown that epitope-tagging Bcl-XL at the NH2 terminus disrupts its ability to interact with CED-4 and this similarly inhibited binding to Apaf-1 (Ref. 9Chinnaiyan A.C. Dixit V.M. Semin. Immunol. 1997; 9: 69-76Crossref PubMed Scopus (94) Google Scholar; Fig. 2 D, left). A previously characterized dicodon mutant form of Bcl-XL(mt7) that does not inhibit cell death did not bind Apaf-1, while an alternate dicodon mutant form Bcl-XL (mt1), which blocks apoptosis but does not heterodimerize with other Bcl-2 family members (29Oltvai Z.N. Millian C.L. Korsmeyer S.J. Cell. 1993; 74: 609-619Abstract Full Text PDF PubMed Scopus (5865) Google Scholar, 30Cheng E.H.-Y. Levine B. Boise L.H. Thompson C.B. Hardwick M. Nature. 1996; 379: 554-556Crossref PubMed Scopus (444) Google Scholar), retained binding to Apaf-1, albeit to a lesser extent (Fig. 2 D, right). Regardless, the data are consistent with the notion that Bcl-XL may function by interacting with Apaf-1. To determine if caspase-9 and Bcl-XL bind to distinct domains in Apaf-1 (3+4), the CED-3-homologous region alone (Apaf-1(3)) and a truncated form that contained only the CED-4-homologous region (Apaf-1(4)) were assessed separately for binding in a co-transfection assay. Caspase-9 bound the CED-3-homologous region (Apaf-1(3); Fig. 2 E, left), while Bcl-XL interacted with the CED-4-homologous region (Apaf-1(4); Fig. 2 E, right). Therefore, caspase-9 and Bcl-XL bind to distinct domains in Apaf-1, raising the possibility that they can form a ternary complex with Apaf-1. To assess this, we asked whether caspase-9 and Bcl-XL might co-precipitate through an endogenous Apaf-1-like activity. 293 cells were co-transfected with caspase-9-Flag and Bcl-XL-Myc. Caspase-9 co-precipitated with Bcl-XL but not a control protein, TRADD-Myc (Fig. 3 A). To confirm that the observed association was indeed mediated by an endogenous Apaf-1-like molecule, the CED-3-homologous domain of Apaf-1 (Apaf-1(3)-Myc) was co-expressed in the same cells. We reasoned that this domain, when present in excess, should competitively inhibit the binding of caspase-9 to endogenous Apaf-1, thereby disrupting the association between caspase-9 and Bcl-XL if the bridging molecule was indeed Apaf-1. As anticipated, Apaf-1(3)-Myc on co-expression attenuated the association of caspase-9-Flag and Bcl-XL-Myc (Fig. 3 B). Furthermore, Apaf-1(3)-Myc was observed in complex with caspase-9-Flag (Fig. 3 B), confirming the competitive nature of the inhibition. Additional validation for ternary complex formation was provided by the observation that overexpressing Bcl-XL-Myc in the same cells did not compete for the association of caspase-9 with Apaf-1(3+4)-Myc (Fig. 3 C). This result is consistent with the existence of independent binding sites on Apaf-1 for caspase-9 and Bcl-XL. The anti-apoptotic ability of Bcl-XL is antagonized by pro-apoptotic members of the Bcl-2 family, including BAX, BAK, and BIK that are capable of forming heterodimers with Bcl-XL (29Oltvai Z.N. Millian C.L. Korsmeyer S.J. Cell. 1993; 74: 609-619Abstract Full Text PDF PubMed Scopus (5865) Google Scholar, 30Cheng E.H.-Y. Levine B. Boise L.H. Thompson C.B. Hardwick M. Nature. 1996; 379: 554-556Crossref PubMed Scopus (444) Google Scholar). Given this, we asked if the pro-apoptotic family members may function by interfering with the ability of Bcl-XL to bind Apaf-1. In keeping with this hypothesis, co-expression of HA-BAX or HA-BAK attenuated the interaction between Bcl-XL-Flag and Apaf-1(3+4)-Myc (Fig. 4 A), with HA-BAX or HA-BAK being found in complex with Bcl-XL-Flag (Fig. 4 A). Consistent with the suggested mechanism, Bcl-XL effectively inhibited BAX-, BIK-, or BAK-induced cell death (Fig. 4 B). Since CED-9 functions upstream of CED-4 and CED-3, Bcl-2 family members likely also function upstream of Apaf-1 and caspase-9 (5Hengartner M.O. Curr. Opin. Genet. Dev. 1996; 6: 34-38Crossref PubMed Scopus (91) Google Scholar). Supporting this viewpoint, we found that cell death induced by BAX, BIK, or BAK was effectively inhibited by dominant negative caspase-9 (Fig. 4 C). In agreement with the notion that activation of caspase-9 serves as a common conduit for the flow of death signals, dominant negative caspase-9 also blocked apoptosis induced by members of the TNF receptor family activated with either cognate ligand or agonist antibody (Fig. 4 D). In conclusion, we have shown that both caspase-9 and Bcl-XLspecifically and simultaneously interact with Apaf-1. Therefore, the formation of a complex involving caspase-9, Apaf-1, and Bcl-XL may play a regulatory role in modulating the mammalian cell death machine. We thank H. Duan for providing the caspase-9 p30-Flag construct; A. M. Chinnaiyan, E. Humke, J. McCarthy, and C. Vincenz for helpful discussion; I. Jones for preparing the figures; and B. Schumann for secretarial assistance.