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Cellular Signalling
journal homepage: www.elsevier.com/locate/cellsig
Review
a r t i c l e
i n f o
Article history:
Received 7 February 2012
Accepted 5 March 2012
Available online 13 March 2012
Keywords:
Apoptosis
Apaf-1
Apoptosome
Caspase activation
a b s t r a c t
Apoptosomes are signaling platforms that initiate the dismantling of a cell during apoptosis. In mammals,
assembly of the apoptosome is the pivotal point in the mitochondrial pathway of apoptosis, and is prompted
by binding of cytochrome c to the apoptotic protease-activating factor 1 (Apaf-1) in the presence of ATP. The
resulting wheel-like heptamer of seven molecules Apaf-1 and seven molecules cytochrome c binds and activates the initiator caspase-9, which in turn ignites the downstream caspase cascade. In this review we discuss
the molecular determinants for the formation of the mammalian apoptosome and caspase activation and
describe the related signaling platforms in ies and nematodes.
2012 Elsevier Inc. All rights reserved.
Contents
1.
Introduction . . . . . . . . . . . . . . . .
2.
Apaf-1 . . . . . . . . . . . . . . . . . . .
3.
Cytochrome c . . . . . . . . . . . . . . .
4.
ATP . . . . . . . . . . . . . . . . . . . .
5.
Structure of the Apaf-1 apoptosome . . . . .
6.
Caspase activation by the Apaf-1 apoptosome
7.
The Apaf-1 orthologs Dark and Ced-4 . . . .
8.
Concluding remarks . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . .
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1. Introduction
Apoptosis is a highly regulated cellular mechanism in metazoans
used to terminate superuous or unwanted cells in a controlled way
[1]. Apoptosis is crucial for normal human embryonic development
[2,3] and the development of the immune system [4]. Deregulation
of apoptosis is associated with severe pathologic conditions, e.g. cancer and neurodegenerative diseases [58]. Two different pathways
have emerged, which both lead to the activation of members of a
class of cystein-dependent aspartate-specic proteases (caspases).
Activation of the caspase cascade ultimately leads to the orderly degradation of the cell [9].
The extrinsic apoptotic pathway is induced by binding of death
ligands to the ectodomains of their cognate death receptors [10]
and leads to the activation of the initiator caspases 8 and 10.
Corresponding author. Tel.: + 49 511 532 8655; fax: + 49 511 532 2909.
E-mail address: eschenburg.susanne@mh-hannover.de (S. Eschenburg).
0898-6568/$ see front matter 2012 Elsevier Inc. All rights reserved.
doi:10.1016/j.cellsig.2012.03.007
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1420
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2. Apaf-1
Upon discovery of the executioner caspase-3 the molecular determinants for its activation were still obscure [16,17]. The molecules,
which eventually activate caspase-3 in the mitochondrial branch of
apoptosis, were subsequently identied as procaspase-9 [18], cytochrome c [19], and Apaf-1 [20]. Apaf-1 was recognized as human
counterpart of Ced-4 of the nematode Caenorhabditis elegans [21].
Based on sequence homology Apaf-1 has been grouped into the
STAND (signal transduction ATPases with numerous domains) family
of proteins [22]. Whether the STAND family constitutes a subfamily of
AAA+ (ATPases associated with diverse cellular activities) ATPases is
debated [23,24]. Apaf-1 is expressed in various tissues and exists in at
least four different splice forms [25]. The residue numbering throughout this review refers to the longest isoform termed Apaf-1-XL (residues 11248). Apaf-1 contains three main domains: the N-terminal
caspase recruitment domain (CARD), the nucleotide binding and oligomerization domain (NOD), and the C-terminal regulatory WD40 repeat domain (WRD) (Fig. 1). The CARD belongs to the death domain
superfamily whose members share a common basic fold consisting
of six bundled -helices [26]. The Apaf-1 CARD binds its counterpart
in procaspase-9 via homotypic interactions mostly involving charged
residues [27]. The NOD (residues 108586) harbors a binding site for
adenine nucleotides and mediates oligomerization of Apaf-1 into the
apoptosome complex.
Several years ago the crystal structure of an N-terminal fragment
of human Apaf-1 comprising the CARD and the NOD was determined
[28]. The structure revealed a compact fold of the NOD and that the
NOD can be divided into four subdomains. These subdomains were
termed nucleotide-binding domain (NBD, residues 108284), helical
domain 1 (HD1, residues 285365), winged-helix domain (WHD, residues 366450), and helical domain 2 (HD2, residues 451586). The
nucleotide binding site of the NOD was occupied with an ADP molecule, which was in contact with residues from all four subdomains.
Since the entire regulatory WRD was missing, the explanation of
how Apaf-1 inhibits itself until cytochrome c binds had to wait until
a crystal structure of full-length Apaf-1 was solved.
The crystal structure of full-length murine Apaf-1 in the absence of
cytochrome c and exogenous nucleotide [29] recently showed that
the tandem -propellers of the WRD do not block the CARD as presumed previously. Rather, the WRD acts as a clamp which holds the
subdomains of the NOD in place. Thus, the WRD prevents the conformational rearrangement of the NOD which is required for apoptosome formation [30,31] (see below for further details).
3. Cytochrome c
The identication of cytochrome c as a crucial component of the
mitochondrial pathway of apoptosis came as a surprise [19]. Given
the well known function of cytochrome c in the respiratory chain, a
role as signaling molecule appeared remarkable. However, the fact
that cytochrome c is, in a healthy cell, conned to the mitochondrial
intermembrane space while the executing part of the apoptosis machinery is located in the cytosol makes the molecule well suited as decisive start signal. The strict spatial separation of signal and
machinery minimizes the chance for accidental activation of the
death cascade.
Apaf-1 is able to bind cytochrome c both in the presence and absence of nucleotide [20,32,33]. It was soon recognized that cytochrome c binds to the WRD and that this interaction is required to
relieve the autoinhibition of Apaf-1 imposed by its WRD, since deletion of the WRD abolishes the need for cytochrome c in the assembly
process [34,35]. Biophysical studies assessing the binding characteristics of cytochrome c to Apaf-1 suggested a stoichiometry of two cytochrome c molecules per molecule Apaf-1 [33,36]. However,
subsequent cryo-EM studies clearly showed a 1:1 stoichiometry
1421
4. ATP
A second crucial molecular event during apoptosome formation is
the exchange of (d)ADP bound to Apaf-1 for exogenous (d)ATP [37].
The origin of the bound diphosphate is still a subject of controversy.
According to a study performed in the lab of Xiadong Wang, monomeric Apaf-1 is loaded with dATP [38]. Here, binding of cytochrome
c prompts Apaf-1 to perform a single round of nucleotide hydrolysis.
The hydrolytic energy would be needed to prime Apaf-1 for the ensuing large conformational changes, which in turn are then triggered by
replacing dADP for exogenous dATP. Several other studies contradict
these ndings showing that recombinant monomeric full-length
Apaf-1 as well as WD40-deleted Apaf-1 puried from different insect
cell strains and from Escherichia coli contain ADP [28,29,39,40]. Consistently, a low but steady (d)ATPase activity of monomeric Apaf-1
in the absence of cytochrome c has been described [4043].
For apoptosome assembly the bound ADP has to be exchanged for
an exogenous nucleoside triphosphate in the presence of cytochrome
c. Not only ATP or dATP but also non-hydrolyzable ATP analogs like
AppNHp or AppCp fulll this function, which emphasizes that chemical energy derived from nucleotide hydrolysis is not required at all
during the assembly process. Rather, the presence of a -phosphate
alone is sufcient to allow apoptosome formation [40].
The molecular effect of the nucleotide exchange is still obscure.
However, comparing the nucleotide binding sites of different AAA+
ATPases and STAND proteins, the notion emerges that the determining factor is a polar interaction of the -phosphate with a sensor residue. This residue is located at the tip of -strand 4 as part of the socalled sensor 1 motif. In AAA+ ATPases the sensor residue is mostly
an asparagine, but serine, threonine, aspartate, or histidine are also
found [44,45]. Several studies suggest that sensor 1 is directly involved in ATP hydrolysis, since its mutation strongly decreases cooperative ATPase activity in different proteins [4648]. Most members
of the AAA+ ATPase related family of STAND ATPases, to which
Apaf-1 belongs, possess an arginine as sensor residue [49,50]. In
Apaf-1 this arginine (R265) would be in interaction distance to the
-phosphate group of an ATP molecule in the nucleotide binding
site [29]. Such an interaction is also visible within crystal structures
of Ced-4, both in the Egl-1 inhibited dimer [51] and in the apoptosome [52], as well as in the EM-derived model of the human apoptosome [31].
The importance of the sensor arginine has been conrmed for
Apaf-1 and other STAND proteins. Functional analysis of an Apaf-1
R265S mutant revealed that the mutant protein does not yield functional apoptosomes [29]. In the bacterial transcription regulator
MalT mutation of the putative sensor arginine R160 to alanine
resulted in loss of activation [53]. The same was observed for the corresponding mutation (R313A) in the plant resistance protein I-2 [54].
1422
1423
Fig. 1. A. Subdomain structure of Apaf-1. Subdomains are color-coded, linkers are shown in gray. B. Conformational states of Apaf-1, the cartoon representation is color coded as in
1A. Top left: Apaf-1 in its autoinhibited state. Top right: Apaf-1 monomer in its assembly competent conformation. The yellow -propeller WD1 has adjusted its position to complete the binding site for cytochrome c between the inner faces of the two -propellers; the blue-turquoise NBDHD1 subunit is rotated to bare the oligomerization interfaces. Bottom: cartoon representation of the apoptosome (PDB code 3IZA). In the three states shown the CARD is not resolved [29,31] and is therefore not shown in the drawing.
1424
8. Concluding remarks
The Apaf-1 apoptosome represents the central signaling hub
within the mitochondrial pathway of apoptosis. In recent years considerable information has been gained about both the architecture
and the function of apoptosomal complexes. Especially structural
analyses using X-ray crystallography and cryo electron microscopy
contributed substantially to the understanding of these molecular
switches. However, there are still open questions about important
aspects of the signal transduction process. The role of the nucleotide
exchange has yet to be determined and the mechanism of caspase
activation is even more subject of controversial discussion. Furthermore, it is still unknown how Apaf-1 interacts with regulating proteins other than cytochrome c. In recent years numerous interaction
partners of Apaf-1 have been identied, which inhibit or stimulate
apoptosome assembly. Detailed knowledge about these interactions, as future studies will certainly deliver, may be the key to target Apaf-1 for therapeutic purposes. The possibility to specically
modulate the function of Apaf-1 is highly desirable, given the central role of Apaf-1 in the mitochondrial pathway of apoptosis.
References
[1] R.C. Taylor, S.P. Cullen, S.J. Martin, Nature Reviews. Molecular Cell Biology 9 (3)
(2008) 231241.
[2] P.M. Domingos, H. Steller, Current Opinion in Genetics & Development 17 (4)
(2007) 294299.
[3] C. Twomey, J.V. McCarthy, Journal of Cellular and Molecular Medicine 9 (2) (2005)
345359.
[4] J.T. Opferman, Cell Death and Differentiation 15 (2) (2008) 234242.
[5] T.G. Cotter, Nature Reviews. Cancer 9 (7) (2009) 501507.
[6] K. Vermeulen, D.R. Van Bockstaele, Z.N. Berneman, Annals of Hematology 84
(10) (2005) 627639.
[7] O. Ekshyyan, T.Y. Aw, Current Neurovascular Research 1 (4) (2004) 355371.
[8] R.M. Friedlander, The New England Journal of Medicine 348 (14) (2003)
13651375.
[9] C.J. de Almeida, R. Linden, Cellular and Molecular Life Sciences 62 (14) (2005)
15321546.
[10] Z. Mahmood, Y. Shukla, Experimental Cell Research 316 (6) (2010) 887899.
[11] W.P. Roos, B. Kaina, Trends in Molecular Medicine 12 (9) (2006) 440450.
[12] S.W. Tait, D.R. Green, Nature Reviews. Molecular Cell Biology 11 (9) (2010)
621632.
[13] G. Kroemer, L. Galluzzi, C. Brenner, Physiological Reviews 87 (1) (2007) 99163.
[14] P. Li, D. Nijhawan, I. Budihardjo, S.M. Srinivasula, M. Ahmad, E.S. Alnemri, X.
Wang, Cell 91 (4) (1997) 479489.
[15] J. Rodriguez, Y. Lazebnik, Genes & Development 13 (24) (1999) 31793184.
[16] M. Tewari, L.T. Quan, K. O'Rourke, S. Desnoyers, Z. Zeng, D.R. Beidler, G.G. Poirier,
G.S. Salvesen, V.M. Dixit, Cell 81 (5) (1995) 801809.
[17] D.W. Nicholson, A. Ali, N.A. Thornberry, J.P. Vaillancourt, C.K. Ding, M. Gallant, Y.
Gareau, P.R. Grifn, M. Labelle, Y.A. Lazebnik, et al., Nature 376 (6535) (1995) 3743.
[18] H. Duan, K. Orth, A.M. Chinnaiyan, G.G. Poirier, C.J. Froelich, W.W. He, V.M. Dixit,
The Journal of Biological Chemistry 271 (28) (1996) 1672016724.
[19] X. Liu, C.N. Kim, J. Yang, R. Jemmerson, X. Wang, Cell 86 (1) (1996) 147157.
[20] H. Zou, W.J. Henzel, X. Liu, A. Lutschg, X. Wang, Cell 90 (3) (1997) 405413.
[21] J. Yuan, H.R. Horvitz, Development 116 (2) (1992) 309320.
[22] D.D. Leipe, E.V. Koonin, L. Aravind, Journal of Molecular Biology 343 (1) (2004)
128.
[23] J.P. Erzberger, J.M. Berger, Annual Review of Biophysics and Biomolecular Structure 35
(2006) 93114.
[24] M. Ammelburg, T. Frickey, A.N. Lupas, Journal of Structural Biology 156 (1) (2006)
211.
[25] M.A. Benedict, Y. Hu, N. Inohara, G. Nunez, The Journal of Biological Chemistry 275
(12) (2000) 84618468.
[26] H.H. Park, Y.C. Lo, S.C. Lin, L. Wang, J.K. Yang, H. Wu, Annual Review of Immunology 25 (2007) 561586.
[27] H. Qin, S.M. Srinivasula, G. Wu, T. Fernandes-Alnemri, E.S. Alnemri, Y. Shi, Nature
399 (6736) (1999) 549557.
[28] S.J. Riedl, W. Li, Y. Chao, R. Schwarzenbacher, Y. Shi, Nature 434 (7035) (2005)
926933.
[29] T.F. Reubold, S. Wohlgemuth, S. Eschenburg, Structure 19 (8) (2011) 10741083.
[30] X. Yu, D. Acehan, J.F. Menetret, C.R. Booth, S.J. Ludtke, S.J. Riedl, Y. Shi, X. Wang,
C.W. Akey, Structure 13 (11) (2005) 17251735.
[31] S. Yuan, X. Yu, M. Topf, S.J. Ludtke, X. Wang, C.W. Akey, Structure 18 (5) (2010)
571583.
[32] A. Saleh, S.M. Srinivasula, S. Acharya, R. Fishel, E.S. Alnemri, The Journal of Biological Chemistry 274 (25) (1999) 1794117945.
[33] C. Purring-Koch, G. McLendon, Proceedings of the National Academy of Sciences
of the United States of America 97 (22) (2000) 1192811931.
[34] Y. Hu, L. Ding, D.M. Spencer, G. Nunez, The Journal of Biological Chemistry 273
(50) (1998) 3348933494.
[35] S.M. Srinivasula, M. Ahmad, T. Fernandes-Alnemri, E.S. Alnemri, Molecular Cell 1
(7) (1998) 949957.
[36] C. Purring, H. Zou, X. Wang, G. McLendon, Journal of the American Chemical Society 121 (32) (1999) 74357436.
[37] S.J. Riedl, G.S. Salvesen, Nature Reviews. Molecular Cell Biology 8 (5) (2007)
405413.
[38] H.E. Kim, F. Du, M. Fang, X. Wang, Proceedings of the National Academy of Sciences of the United States of America 102 (49) (2005) 1754517550.
[39] Q. Bao, W. Lu, J.D. Rabinowitz, Y. Shi, Molecular Cell 25 (2) (2007) 181192.
[40] T.F. Reubold, S. Wohlgemuth, S. Eschenburg, The Journal of Biological Chemistry
284 (47) (2009) 3271732724.
[41] X. Jiang, X. Wang, The Journal of Biological Chemistry 275 (40) (2000) 3119931203.
[42] Y. Hu, M.A. Benedict, L. Ding, G. Nunez, The EMBO Journal 18 (13) (1999) 35863595.
[43] H. Zou, Y. Li, X. Liu, X. Wang, The Journal of Biological Chemistry 274 (17) (1999)
1154911556.
[44] A.N. Lupas, J. Martin, Current Opinion in Structural Biology 12 (6) (2002) 746753.
[45] J. Snider, G. Thibault, W.A. Houry, Genome Biology 9 (4) (2008) 216.
[46] D.A. Hattendorf, S.L. Lindquist, The EMBO Journal 21 (12) (2002) 1221.
[47] K. Karata, T. Inagawa, A.J. Wilkinson, T. Tatsuta, T. Ogura, The Journal of Biological
Chemistry 274 (37) (1999) 2622526232.
[48] G.J. Steel, C. Harley, A. Boyd, A. Morgan, Molecular Biology of the Cell 11 (4) (2000)
13451356.
[49] O. Danot, E. Marquenet, D. Vidal-Ingigliardi, E. Richet, Structure 17 (2) (2009) 172182.
1425
[74] L.A. Allan, N. Morrice, S. Brady, G. Magee, S. Pathak, P.R. Clarke, Nature Cell Biology
5 (7) (2003) 647654.
[75] L.A. Allan, P.R. Clarke, Molecular Cell 26 (2) (2007) 301310.
[76] A. Seifert, L.A. Allan, P.R. Clarke, The FEBS Journal 275 (24) (2008) 62686280.
[77] H. Kanuka, K. Sawamoto, N. Inohara, K. Matsuno, H. Okano, M. Miura, Molecular
Cell 4 (5) (1999) 757769.
[78] A. Rodriguez, H. Oliver, H. Zou, P. Chen, X. Wang, J.M. Abrams, Nature Cell Biology
1 (5) (1999) 272279.
[79] L. Zhou, Z. Song, J. Tittel, H. Steller, Molecular Cell 4 (5) (1999) 745755.
[80] S. Yuan, X. Yu, M. Topf, L. Dorstyn, S. Kumar, S.J. Ludtke, C.W. Akey, Structure 19
(1) (2011) 128140.
[81] A. Oberst, C. Bender, D.R. Green, Cell Death and Differentiation 15 (7) (2008)
11391146.
[82] R.J. Krieser, K. White, Apoptosis 14 (8) (2009) 961968.
[83] E. Arama, J. Agapite, H. Steller, Developmental Cell 4 (5) (2003) 687697.
[84] E. Arama, M. Bader, M. Srivastava, A. Bergmann, H. Steller, The EMBO Journal 25
(1) (2006) 232243.
[85] C.S. Mendes, E. Arama, S. Brown, H. Scherr, M. Srivastava, A. Bergmann, H. Steller,
B. Mollereau, EMBO Reports 7 (9) (2006) 933939.
[86] E. Abdelwahid, T. Yokokura, R.J. Krieser, S. Balasundaram, W.H. Fowle, K. White,
Developmental Cell 12 (5) (2007) 793806.
[87] L. Dorstyn, K. Mills, Y. Lazebnik, S. Kumar, The Journal of Cell Biology 167 (3)
(2004) 405410.
[88] L. Dorstyn, S. Read, D. Cakouros, J.R. Huh, B.A. Hay, S. Kumar, The Journal of Cell
Biology 156 (6) (2002) 10891098.
[89] J.C. Means, I. Muro, R.J. Clem, Cell Death and Differentiation 13 (7) (2006)
12221234.
[90] J. Varkey, P. Chen, R. Jemmerson, J.M. Abrams, The Journal of Cell Biology 144 (4)
(1999) 701710.
[91] K.C. Zimmermann, J.E. Ricci, N.M. Droin, D.R. Green, The Journal of Cell Biology
156 (6) (2002) 10771087.
[92] L. Dorstyn, S. Kumar, Cell Death and Differentiation 15 (3) (2008) 461470.
[93] X. Yu, L. Wang, D. Acehan, X. Wang, C.W. Akey, Journal of Molecular Biology 355
(3) (2006) 577589.
[94] N. Yan, J.R. Huh, V. Schirf, B. Demeler, B.A. Hay, Y. Shi, The Journal of Biological
Chemistry 281 (13) (2006) 86678674.
[95] R. Wilson, L. Goyal, M. Ditzel, A. Zachariou, D.A. Baker, J. Agapite, H. Steller, P.
Meier, Nature Cell Biology 4 (6) (2002) 445450.
[96] H.D. Ryoo, A. Bergmann, H. Gonen, A. Ciechanover, H. Steller, Nature Cell Biology
4 (6) (2002) 432438.
[97] M.S. Spector, S. Desnoyers, D.J. Hoeppner, M.O. Hengartner, Nature 385 (6617)
(1997) 653656.
[98] N. Yan, L. Gu, D. Kokel, J. Chai, W. Li, A. Han, L. Chen, D. Xue, Y. Shi, Molecular Cell
15 (6) (2004) 9991006.