New insights into apoptosome structure and function

Abstract

The apoptosome is a platform that activates apical procaspases in response to intrinsic cell death signals. Biochemical and structural studies in the past two decades have extended our understanding of apoptosome composition and structure, while illuminating the requirements for initiator procaspase activation. A number of studies have now provided high-resolution structures for apoptosomes from C. elegans (CED-4), D. melanogaster (Dark), and H. sapiens (Apaf-1), which define critical protein interfaces, including intra and interdomain interactions. This work also reveals interactions of apoptosomes with their respective initiator caspases, CED-3, Dronc and procaspase-9. Structures of the human apoptosome have defined the requirements for cytochrome c binding, which triggers the conversion of inactive Apaf-1 molecules to an extended, assembly competent state. While recent data have provided a detailed understanding of apoptosome formation and procaspase activation, they also highlight important evolutionary differences with functional implications for caspase activation. Comparison of the CARD/CARD disks and apoptosomes formed by CED-4, Dark and Apaf-1. Cartoons of the active states of the CARD-CARD disks, illustrating the two CED-4 CARD tetrameric ring layers (CED4a and CED4b; top row) and the binding of 8 Dronc CARDs and between 3-4 pc-9 CARDs, to the Dark and Apaf-1 CARD disk respectively (middle and lower rows). Ribbon diagrams of the active CED-4, Dark and Apaf-1 apoptosomes are shown (right column).

Fig. 1

Evolutionarily conserved and divergent features of apoptosomes. a A schematic representation of C.elegans CED-4, Drosophila Dark and human Apaf-1. In Dark and Apaf-1, the last blade in the 8-blade β-propeller is formed by the HD2 linker (blue region). Protein domains are color-coded and are drawn approximately to scale. b The ground state CED-4 apoptosome is shown as a ribbon diagram with a color-coded subunit and two stacked, four CARD rings, in top and side views (PDB 3LQR). c Details of the interdigitated and stacked four CARD rings are shown with CARD-A in light green and CARD-B in blue. Linker helix 7 is marked (α7). d A top view of the Dark apoptosome is shown in a possible post-activation state (PDB 3J9K) with the Dark-Dronc CARD crown (Dronc CARD in purple). e The Dark-Dronc crown is shown at higher magnification in top and side views. f A top view of the active Apaf-1 apoptosome is shown with an 8 CARD disk (PDB 5JUY). g Top and side views are shown of the 8 CARD disk annotated with positions of Apaf-1 CARDs and pc-9 CARDs (in purple) that form a left-handed spiral for Apaf-1/pc-9 CARD pairs. Respective scale bars for b, d, f, and for c, e, g are shown

Fig. 2

Apical procaspase diagrams and a comparison of CARD disks formed by Apaf-1 and pc-9 CARDs. a A schematic representation is shown for apical procaspases from C. elegans, D. melanogaster, and H. sapiens. Domains are color-coded with linker regions highlighted in gold. b, c Top and side views are shown of an Apaf-1/pc-9 8 CARD disk from an active human apoptosome (PDB 5JUY). CARD pairs 1a/2p, 3a/4p, 5a/6p, and 7a/8p are labeled. A seam or dislocation in the helical lattice between 1a/7a and 2p/8p is indicated in b. d An overlay is shown of two 8 CARD disk structures with the more recent model in gray (PDB 5WVE). e A top view is shown of a 6 CARD spiral from a crystal structure (PDB 5WVC) annotated with the relevant positions in the CARD disk from the apoptosome. f, g Overlays are shown between the 6 CARD spiral and an 8 CARD disk after aligning them on position 2p. The match between the two structures becomes somewhat worse as one moves around the left-handed spiral with the Apaf-1 CARD at position 7a in the 6 CARD spiral displaced vertically from its counterpart in the disk

Fig. 3

Assembly paths for ground state and active human apoptosomes. An extended Apaf-1 monomer (not shown to scale) may assemble with other monomers to form a heptameric apoptosome in the ground state with disordered Apaf-1 CARDs. However, in the presence of pc-9 two active platforms may be formed as shown (active state 1 and 2). In addition it may also be possible to form a third hybrid active platform with both p20/p10 and three CARD modules bound to the central hub (not shown, see Fig. 5e)

Fig. 4

Comparison of two structures of the active Apaf-1 apoptosome with a symmetry mismatch between the CARD disk and the platform. a A top view is presented of an active apoptosome with the platform in gray ribbons (PDB 5JUY) within the relevant density map. An acentric 8 CARD disk and density for the four CARD-NBD linkers (gold) are shown. A region of density (blue) identified as a p20/p10 catalytic domain of pc-9 is located on the central hub [5]. b A model for an active platform with an 8 CARD disk and a three CARD module on the central hub (PDB 5WVE) [7]. c A close-up view of a, with density for the p20/p10 catalytic domain omitted and a second possible position for this feature indicated (dashed oval; see text and ref. [5] for details). Linker densities in gold are positioned to connect Apaf-1 CARDs in positions 1a, 3a, 5a, and 7a with helix α8 in the NBDs of subunits 1, 3, 5, and 7. d A close-up view of b is shown with relevant CARD-NBD linkers as black lines to their respective Apaf-1 subunits. Apaf-1 CARDs in the three CARD module are shown in gold

Fig. 5

Models of procaspase-9 activation on the Apaf-1 apoptosome. At least six permutations are possible with pc-9 CARDs docked via 7 and 8 CARD disks, and a three CARD module on the central hub. a, b Three pc-9 molecules with a 7 CARD disk on the platform. c, d Four pc-9 molecules with an 8 CARD disk on the central hub. e, f Five pc-9 molecules with an 8 CARD disk on the platform