Intrinsic apoptotic signaling pathway module

Cell-intrinsic stress signals regulate BCL2-family mitochondrial permeabilization, cytochrome c release, apoptosome assembly, and initiator caspase-9 activation.

Curated compact signaling-pathway module generated from verified UniProt exemplar accessions and local PAINT IBD rows. PTN anchors are included only when the exemplar accession appears in an IBD seed row in interpro/panther; roles without local PAINT seeds remain grounded by verified UniProt exemplar accessions. Falcon integration (2026-06-28): Falcon findings are linked as evidence and family-level support. Automatically extracted open-question headings were intentionally not retained as knowledge_gap entries because they were not manually curated. Machine-generated Falcon citations remain curation support and are not manually adjudicated here. Manual APOPTOSIS audit (2026-09-30): the BCL2/MOMP, CYCS/APAF1/CASP9, and downstream execution boundaries were checked against completed human, mouse, worm, fly, and fungal apoptosis reviews. This module remains a valid intrinsic-signaling seed. The BCL2-family and execution-phase handoff now have companion draft modules; this seed should stay draft until mammalian apoptosome scoping is modeled explicitly. CANDIDATE ASSESSED, NOT MODELLED - condition-dependent CASP9 CARD higher-order assembly (PMID:42819741): a 2026 structural/biophysical study reports a 2.4 A crystal structure of the isolated human caspase-9 CARD (PDB 9R44) forming a sulfate-mediated dimer-of-dimers on a conserved arginine-rich surface (R10, R13, R15, R52, R56), notes that this surface overlaps the C9 CARD filament interface (PDB 9S6F) and, for the subset R13/R52, the APAF-1 CARD interface (PDB 4RHW), and shows reversible temperature-dependent filament/droplet transitions plus AF3 predictions that filament propensity may extend to other human CARDs. It is deliberately not modelled as a part, a mechanism or a knowledge gap of this module, for four reasons. (i) No new participant: CASP9 (casp9_caspase_9_initiator_protease) and APAF1 (apaf1_apaf1_apoptosome_scaffold) are already annotons here, so this is not a membership change - it is finer structural detail on a protein the module already carries. (ii) No revision to the modelled step: the new structure is the isolated CARD with no binding partner, and the APAF-1-bound interface it is compared against comes from previously published complexes (3YGS, 3JUY, 4RHW, 5WVC, 5WVE), which are what the existing apoptosome_assembly -> caspase_9_activation connection already rests on. The shared arginine subset is a reuse observation about a known interface, not a new causal link. (iii) Conditions: the dimer-of-dimers came from 1.5 M lithium sulfate, which the authors call a non-physiological crystallization condition; DLS shifts are explicitly stoichiometry-blind, SEC showed no new peak, CEST resolved no substantially populated second state, and the reversible filament-to-droplet transition required ~650 uM protein, with the filamentous state forming only at 4 degrees C, which the authors note is not physiologically relevant. Under physiological conditions the CARD is predominantly monomeric. The authors' own conclusion is that the crystallographic assembly is "a sulfate-stabilized, structurally accessible assembly state rather than a dominant solution species". (iv) Claim strength: the limitations section states that the assembly states "are characterized under in vitro conditions, and their physiological relevance remains to be established", and the AF3 predictions "require direct experimental validation"; notably AF3-guided EM found APAF-1 CARD itself forming amorphous aggregates rather than filaments. Adding a CASP9 self-assembly step on this basis would assert a mechanism upstream of, or parallel to, apoptosome recruitment that the study does not claim. No knowledge_gaps entry either: "is CARD phase behaviour physiologically relevant" is a question about CARD biophysics generally rather than about this module's apoptosome wiring, and it is the authors' own stated next step rather than a gap this curation identified. The CARD-CARD recruitment biology is already curated at gene level in genes/human/CASP9 and genes/human/APAF1, where the uninformative protein-binding rows were MODIFYed to GO:0050700 CARD domain binding. Re-evaluate if cellular work establishes that CASP9 CARD self-association or condensate formation occurs in cells and modulates apoptosome-dependent CASP9 activation; the arginine-hotspot mutant (R10E/R52E/R56E) characterised here is the obvious reagent for that test.