Inhibitor of apoptosis proteins in eukaryotic evolution and development: a model of thematic conservation

Abstract

The past decade and a half has witnessed the discovery of a large, evolutionarily conserved family of cellular genes bearing homology to the prototype baculovirus Inhibitor of Apoptosis (IAP). The logical decision in the field to also refer to these cellular proteins as IAPs fails to do justice to this versatile group of factors that play a wide range of roles in eukaryotic development and homeostasis which include, but are not limited to, the regulation of programmed cell death. Here we describe the shared functional characteristics of several well-characterized IAPs whose defining motifs place them more in the category of multifunctional modular protein interaction domains.

Figure 1. Domain structure of the IAP protein family

The characteristic BIR domains are indicated by red rectangles, CARD domains by purple rectangles, RING domains by green ovals, NBD domains by diamonds, LRR domains by teal circles, and UBC domains by yellow hexagons. DIAP1, DIAP2, Deterin, and dBruce are Drosophila IAPs, while SfIAP1 and TnIAP are lepidopteran IAPs. Abbreviations: IAP, inhibitor of apoptosis; XIAP, X-linked IAP; BIRC, baculoviral IAP repeat containing; hILP, human IAP-like protein; Ts-IAP, testis-specific IAP; c-IAP, cellular IAP; ML-IAP, melanoma-IAP; NAIP, neuronal apoptosis inhibitory protein; DIAP, Drosophila IAP; SfIAP1, Spodoptera frugiperda IAP; TnIAP, Trichoplusia ni IAP; CeBIR-1,-2, Caenorhabditis elegans BIRC SpIAP, Schizosaccharomyces pombe IAP; ScIAP, Saccharomyces cerevisiae IAP; BIR, baculoviral IAP repeat; CARD, caspase recruitment domain; NBD, nucleotide binding oligomerization domain; LRR, leucine rich repeat.

Figure 2. The caspase-binding elements of IAPs

Structure of the complex between XIAP BIR3 and caspase-9 (left, PDB 1NW9) and XIAP BIR2 with caspase-3 (right, PDB 1I3O). The caspase is in surface representation (large subunit in blue, small subunit in grey). The XIAP BIR domain and flanking region are in green cartoon, with the co-ordinated zinc in pink. Caspase inhibition is achieved via two-binding sites: an anchoring interaction with the BIR surface groove, and an “Inhibitory interaction”. Insets: critical XIAP residues that interact with the caspase are in cyan stick representation. Critical caspase residues that interact with XIAP are in orange surface representation. Primary sequence alignment reveals that the BIR surface groove is common to most IAP BIR domains, and there is overlapping binding specificity between IAP BIR domains. The BIR surface groove binds IAP-binding motif (IBM) containing proteins including caspase-9 and -3 (shown here in inset, N-terminus of caspase small subunit in grey stick), caspase-7, Smac/DIABLO, HtrA2/Omi, Grim, Reaper, Hid and others. Alignment of primary sequence across the “Inhibitory interaction” site demonstrates that XIAP is the only IAP that contains all the critical residues to confer direct inhibition of caspase catalytic activity. Although ILP2 also contains all the caspase-9 inhibitory elements, it is an unstable protein whose endogenous expression is yet to be demonstrated.

Figure 3. IAP-dependent regulation of conserved Drosophila and mammalian signaling pathways

Inhibition of apoptosis in Drosophila cells by DIAP1 occurs through binding to the initiator and effector caspases, Dronc and DrICE. Similarly, direct binding and inhibition of caspase-3 in mammalian cells is mediated by XIAP. Mammalian c-IAP1 and c-IAP2 can directly bind caspases but are poor caspase inhibitors, instead acting to regulate apoptosis by indirectly modulating caspase-8 activity. Binding of TNF to its receptor results in recruitment of TRADD, RIP, and TRAF2. The cIAPs also participate in pro-survival signaling through TNFR by associating with TRAF2. C-IAP1 and -2 ubiquitinate RIP1, minimizing association with caspase-8 and preventing apoptosis. Additionally the association of RIP, TRAF2, and cIAP1/2 leads to the activation of TAK and subsequent NF-κB and JNK activation, resulting in enhanced transcription of pro-survival genes. C-IAP1 and -2 can also inhibit NIK kinase and downstream processing of p100, thereby negatively regulating NF-κB activation. Thus, the effects of c-IAP1 and -2-dependent signaling on NF-κB are likely context dependent. A TNFR-like pathway regulates immune responses to microbial infection in Drosophila. Peptidoglycan from Gram-negative bacteria is recognized by peptidoglycan recognition proteins (PGRP), which can activate the IMD signaling pathway. IMD is an insect homolog of mammalian RIP1. Genetic studies place IMD, dFADD, Dredd and DIAP2 upstream of or parallel to dTAK activation. DTAK activates both the JNK and Relish pathways analogously to TAK1 in mammalian cells, promoting induction of anti-microbial peptide genes.