Mammalian apoptotic execution: proteolysis, ICAD/CAD and contextual nuclear branches

Mammalian executioner caspases cleave distinct sets of cellular substrates. CASP3 cleavage of ICAD relieves inhibition of the CAD nuclease after ICAD-supported folding, enabling chromatin DNA fragmentation; mouse CASP7 provides a supported alternative ICAD-cleaving activity. XIAP and mitochondrial SMAC regulate execution in a cell-dependent manner. CASP6 proteolysis, Acinus-associated nuclear remodeling and AIF chromatin engagement are separately qualified branches, not an obligatory sequence shared by every dying cell. The template starts downstream of initiation and excludes a complete substrate inventory and phagocyte-mediated disposal.

MODULE:apoptotic_execution_phaseDRAFTABSTRACTBiological Processmodules/apoptotic_execution_phase.yaml

execution phase of apoptosisGO:0097194

PMID:23457257

Comparative network evolution constrains transfer across metazoan lineages.

PMID:38824481

Mouse genetics contextualizes executioner-caspase requirements.

PMID:24890510

Review links ICAD-dependent folding and nuclease release to nuclear DNA degradation.

PMID:18309324

Non-apoptotic functions prevent interpreting every knockout phenotype as execution evidence.

PMID:18414036

Direct anti-caspase activity of mammalian XIAP is not a family-wide property of IAP proteins.

The original human-only template is expanded through verified human/mouse subfamily representatives. CASP3/CASP7/CASP6 are distinct roles; XIAP is not generalized to all BIR proteins or all executioners. ICAD folding and inhibition are split and connected with appropriate signs. AIF has no generic CASP3 causal incoming edge, and Acinus RNA binding is not presented as its condensation mechanism. Family labels are copied verbatim from the official PANTHER ontology, including the unusual official DFFA label. Sixteen human/mouse representatives have individual reviews. Independent integration QA distinguishes biochemical capacity, native perturbation evidence and broader family membership; Mammalia scope does not transfer every assay-specific relationship to all mammals.

12Nodes

9Parts

1Variant Sets

2Variants

10Annotons

10Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:apoptotic_execution_phase deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ representative grounding skipped for abstract module.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

17 gene-function check(s) reflected in core functions · 0 conflict(s) · 11 evidence or coverage gap(s) (28 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

Annoton	Participant	Function	Assessment
casp3_executioner	CASP3 (human) UniProtKB:P42574 Family Representative	cysteine-type endopeptidase activity GO:0004197	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
casp3_executioner	Casp3 (mouse) UniProtKB:P70677 Family Representative	cysteine-type endopeptidase activity GO:0004197	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
casp7_executioner	CASP7 (human) UniProtKB:P55210 Family Representative	cysteine-type endopeptidase activity GO:0004197	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
casp7_executioner	Casp7 (mouse) UniProtKB:P97864 Family Representative	cysteine-type endopeptidase activity GO:0004197	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
casp6_executioner	CASP6 (human) UniProtKB:P55212 Family Representative	cysteine-type endopeptidase activity GO:0004197	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
casp6_executioner	Casp6 (mouse) UniProtKB:O08738 Family Representative	cysteine-type endopeptidase activity GO:0004197	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
xiap_caspase_inhibitor	XIAP (human) UniProtKB:P98170 Family Representative	cysteine-type endopeptidase inhibitor activity GO:0004869	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
xiap_caspase_inhibitor	Xiap (mouse) UniProtKB:Q60989 Family Representative	cysteine-type endopeptidase inhibitor activity GO:0004869	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
diablo_iap_antagonist	DIABLO (human) UniProtKB:Q9NR28 Family Representative	BIR domain binding GO:1990525	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
diablo_iap_antagonist	Diablo (mouse) UniProtKB:Q9JIQ3 Family Representative	BIR domain binding GO:1990525	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dffa_cad_chaperone	DFFA (human) UniProtKB:O00273 Family Representative	protein folding chaperone GO:0044183	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dffa_cad_chaperone	Dffa (mouse) UniProtKB:O54786 Family Representative	protein folding chaperone GO:0044183	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dffa_icad_inhibitor_chaperone	DFFA (human) UniProtKB:O00273 Family Representative	deoxyribonuclease inhibitor activity GO:0060703	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dffa_icad_inhibitor_chaperone	Dffa (mouse) UniProtKB:O54786 Family Representative	deoxyribonuclease inhibitor activity GO:0060703	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dffb_cad_dnase	DFFB (human) UniProtKB:O76075 Family Representative	DNA endonuclease activity GO:0004520	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dffb_cad_dnase	Dffb (mouse) UniProtKB:O54788 Family Representative	DNA endonuclease activity GO:0004520	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
acin1_chromatin_condensation	ACIN1 (human) UniProtKB:Q9UKV3 Family Representative	caspase-activated chromatin-condensation-promoting activity No function ID	No Function Id A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
aifm1_chromatin_engagement	AIFM1 (human) UniProtKB:O95831 Family Representative	DNA binding GO:0003677	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
casp3_executioner	caspase-3 subfamily PANTHER:PTHR10454:SF198 Family	cysteine-type endopeptidase activity GO:0004197	Family Review Missing No supported structured family review is available for PANTHER:PTHR10454:SF198.
casp7_executioner	caspase-7 subfamily PANTHER:PTHR10454:SF31 Family	cysteine-type endopeptidase activity GO:0004197	Family Review Missing No supported structured family review is available for PANTHER:PTHR10454:SF31.
casp6_executioner	caspase-6 subfamily PANTHER:PTHR10454:SF206 Family	cysteine-type endopeptidase activity GO:0004197	Family Review Missing No supported structured family review is available for PANTHER:PTHR10454:SF206.
xiap_caspase_inhibitor	XIAP subfamily PANTHER:PTHR10044:SF115 Family	cysteine-type endopeptidase inhibitor activity GO:0004869	Family Review Missing No supported structured family review is available for PANTHER:PTHR10044:SF115.
diablo_iap_antagonist	SMAC/DIABLO subfamily PANTHER:PTHR32247:SF3 Family	BIR domain binding GO:1990525	Family Review Missing No supported structured family review is available for PANTHER:PTHR32247:SF3.
dffa_cad_chaperone	ICAD/DFFA subfamily PANTHER:PTHR12306:SF16 Family	protein folding chaperone GO:0044183	Family Review Missing No supported structured family review is available for PANTHER:PTHR12306:SF16.
dffa_icad_inhibitor_chaperone	ICAD/DFFA subfamily PANTHER:PTHR12306:SF16 Family	deoxyribonuclease inhibitor activity GO:0060703	Family Review Missing No supported structured family review is available for PANTHER:PTHR12306:SF16.
dffb_cad_dnase	CAD/DFFB subfamily PANTHER:PTHR13067:SF2 Family	DNA endonuclease activity GO:0004520	Family Review Missing No supported structured family review is available for PANTHER:PTHR13067:SF2.
acin1_chromatin_condensation	Acinus subfamily PANTHER:PTHR46589:SF1 Family	caspase-activated chromatin-condensation-promoting activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
aifm1_chromatin_engagement	AIFM1 subfamily PANTHER:PTHR43557:SF4 Family	DNA binding GO:0003677	Family Review Missing No supported structured family review is available for PANTHER:PTHR43557:SF4.

Feedback loops (advisory, prose-driven: a regulator counts as "feedback" when its own description says so)

✓ every negative regulator described as feedback has an upstream edge closing the loop.

iap_caspase_restraint ⊣ casp3_proteolysis [input]
iap_caspase_restraint is a negative regulator with no upstream edge (not described as feedback)
mitochondrial_iap_antagonism ⊣ iap_caspase_restraint [input]
mitochondrial_iap_antagonism is a negative regulator with no upstream edge (not described as feedback)
casp3_proteolysis ⊣ cad_inhibition [input]
casp3_proteolysis is a negative regulator with no upstream edge (not described as feedback)
cad_inhibition ⊣ dff_dna_fragmentation [input]
cad_inhibition is a negative regulator with no upstream edge (not described as feedback)
casp7_proteolysis ⊣ cad_inhibition [input]
casp7_proteolysis is a negative regulator with no upstream edge (not described as feedback)

Gene-review completeness (16/16 grounded genes reviewed)

2 complete review(s) · 3 with deep research · 0 missing review · 13 reviewed but lacking deep research

Gene	Review	Complete	Deep research
ACIN1 Q9UKV3	✓	43/46	✓
AIFM1 O95831	✓	64/77	✗
CASP3 P42574	✓	190/199	✓
Casp3 P70677	✓	184/200	✓
Casp6 O08738	✓	55/71	✗
CASP6 P55212	✓	252/257	✗
CASP7 P55210	✓	98/101	✗
Casp7 P97864	✓	78/84	✗
DFFA O00273	✓	✓	✗
Dffa O54786	✓	33/34	✗
Dffb O54788	✓	41/46	✗
DFFB O76075	✓	44/45	✗
Diablo Q9JIQ3	✓	32/36	✗
DIABLO Q9NR28	✓	✓	✗
XIAP P98170	✓	219/223	✗
Xiap Q60989	✓	66/67	✗

Tree

Mammalian apoptotic execution with contextual branchesBiological Processapoptotic_execution_phase

Parts
1. 1. Principal executioner proteolysis
2. CASP3 or CASP7 executioner contributionRegulatory Stepexecutioner_caspase_proteolysis
  
  Variants
  1. One or both principal executioner contributions by executioner caspase (One Or More)
    
    CASP3 executioner proteolysisRegulatory Stepcasp3_proteolysis
    
    Annotons
    
    CASP3 principal executioner caspase Family: caspase-3 subfamily
    
    CASP7 substrate-selective proteolysisRegulatory Stepcasp7_proteolysis
    
    Annotons
    
    CASP7 executioner caspase Family: caspase-7 subfamily
3. 2. Context-dependent CASP6 proteolysis optional
4. Context-dependent CASP6 proteolysisRegulatory Stepcasp6_proteolysis
  
  Annotons
  - CASP6 executioner and amplifier caspase Family: caspase-6 subfamily
5. 3. XIAP restraint of active CASP3/CASP7 optional
6. XIAP restraint of active CASP3/CASP7Regulatory Stepiap_caspase_restraint
  
  Annotons
  - XIAP caspase inhibitor Family: XIAP subfamily
7. 4. Mitochondrial SMAC/DIABLO antagonism optional
8. Mitochondrial SMAC/DIABLO antagonismRegulatory Stepmitochondrial_iap_antagonism
  
  Annotons
  - DIABLO/SMAC IAP antagonist Family: SMAC/DIABLO subfamily
9. 5. ICAD-dependent CAD folding optional
10. ICAD-dependent CAD foldingRegulatory Stepcad_folding
  
  Annotons
  - DFFA CAD-folding chaperone Family: ICAD/DFFA subfamily
11. 6. ICAD inhibition of CAD nuclease optional
12. ICAD inhibition of CAD nucleaseRegulatory Stepcad_inhibition
  
  Annotons
  - DFFA/ICAD DNase inhibitor Family: ICAD/DFFA subfamily
13. 7. CAD chromatin DNA cleavage optional
14. CAD chromatin DNA cleavageRegulatory Stepdff_dna_fragmentation
  
  Annotons
  - DFFB/CAD apoptotic DNase Family: CAD/DFFB subfamily
15. 8. Contextual Acinus nuclear remodeling optional
16. Contextual Acinus nuclear remodelingRegulatory Stepacinus_remodeling
  
  Annotons
  - ACIN1 apoptotic chromatin condensation factor Family: Acinus subfamily
17. 9. Contextual AIF chromatin engagement optional
18. Contextual AIF chromatin engagementRegulatory Stepaif_chromatin_engagement
  
  Annotons
  - AIFM1 pro-apoptotic chromatin engagement Family: AIFM1 subfamily

Details

Context

MammaliaNCBITaxon:40674

cytosolGO:0005829 nucleusGO:0005634 mitochondrial intermembrane spaceGO:0005758

PMID:23457257

Comparative review documents lineage-specific expansion and loss rather than a universally identical animal network.

PMID:17343828

DFF comparative genomics shows conserved architecture with losses in several sampled animal lineages.

PMID:38824481

Mouse studies reveal tissue, genotype and non-apoptotic variation.

Mammalian apoptotic execution with contextual branchesBiological Processapoptotic_execution_phase

Human and mouse exemplars ground a mammalian template. Part numbering is organizational, not temporal. A required CASP3/CASP7 variant set encodes at least one principal executioner contribution; neither protease is individually obligatory. CASP6, regulators and nuclear branches are optional additions, and their optional flags do not assert dispensability within every assay. AIF-associated caspase-independent death alone is outside this caspase-mediated implementation. ICAD-dependent folding and disinhibition are internal requirements of the represented CAD route, while CAD-mediated DNA fragmentation is not required for all apoptotic death. Upstream caspase activation and AIF release mechanisms are boundary inputs.

execution phase of apoptosisGO:0097194

Context

MammaliaNCBITaxon:40674

cytosolGO:0005829 nucleusGO:0005634 mitochondrial intermembrane spaceGO:0005758

PMID:23457257

Comparative review documents lineage-specific expansion and loss rather than a universally identical animal network.

PMID:17343828

DFF comparative genomics shows conserved architecture with losses in several sampled animal lineages.

PMID:38824481

Mouse studies reveal tissue, genotype and non-apoptotic variation.

Connections

iap_caspase_restraint -> casp3_proteolysis Negatively Regulates

XIAP linker/BIR2 sterically inhibits active CASP3; this is not generalized to every executioner caspase.

PMID:11257232

Direct human CASP3-XIAP structure supports the inhibitory interaction.

iap_caspase_restraint -> casp7_proteolysis Negatively Regulates

XIAP linker/BIR2 restrains active CASP7 through a defined substrate-cleft blockade.

PMID:11257231

Structure and biochemistry identify the inhibitory linker/BIR2 mechanism.

mitochondrial_iap_antagonism -> iap_caspase_restraint Negatively Regulates

Processed SMAC can antagonize XIAP, conditional on protein architecture and cellular competence; mitochondrial release is not a sufficient universal switch.

PMID:14512414

BIR2/BIR3 architecture determines relief of inhibition in vitro.

PMID:14623868

Native sympathetic-neuron experiments show that endogenous SMAC release can be insufficient.

casp3_proteolysis -> cad_inhibition Negatively Regulates

CASP3 cleaves ICAD, disabling its restraint of CAD. This edge describes destruction of an inhibitory activity rather than activation of ICAD.

PMID:9108473

DFF45 cleavage by caspase-3 produces an active DNA-fragmenting factor.

PMID:9671700

Cleaved DFF45 fragments dissociate from active DFF40.

PMID:9422506

Caspase-3 treatment of recombinant mouse CAD/ICAD complex releases DNase activity.

cad_inhibition -> dff_dna_fragmentation Negatively Regulates

Intact ICAD restrains CAD DNA cleavage even when the complex can bind DNA.

PMID:15572351

Reconstituted DFF is DNA-binding competent but catalytically inhibited.

PMID:9422506

Mouse CAD inhibition by recombinant ICAD directly supports the sign of this relationship.

cad_folding -> dff_dna_fragmentation Provides Input For

ICAD chaperoning produces folding-competent CAD that can later be released from inhibition. Folding alone is not activation.

PMID:9671700

Coexpression of DFF40 and DFF45 is required for recombinant active DFF.

PMID:19944011

Chaperoning and inhibition have separable structural requirements.

PMID:10336474

Productive CAD synthesis depends on ICAD-L in the reported folding assays; this is preparation of the nuclease, not its subsequent release from inhibition.

casp3_proteolysis -> acinus_remodeling Positively Regulates

CASP3 cleavage licenses the Acinus activity in the original assay; this does not assert universal Acinus necessity for condensation.

Context

Homo sapiensNCBITaxon:9606

experimental contexts supporting cleavage-dependent Acinus activity

PMID:10490026

Cleaved Acinus promotes condensation in the original cell-free experiments.

PMID:16537548

Later knockdown experiments limit any universal requirement.

casp7_proteolysis -> cad_inhibition Negatively Regulates

Mouse CASP7 cleaves and inactivates ICAD in the reported biochemical comparison. Casp7 expression and activation correlate with retained DNA fragmentation in C57BL/6J Casp3-null precursor neurons; the same efficiency is not asserted for human CASP7 or every mouse tissue.

Context

Mus musculusNCBITaxon:10090

mouse ICAD-cleavage assays and strain-dependent Casp3-null neuronal context

PMID:15525783

Direct mouse-versus-human enzyme comparison establishes the mouse ICAD-cleaving capacity; neuronal results provide contextual correlation, not universal rescue sufficiency.

casp3_proteolysis -> casp6_proteolysis Positively Regulates

CASP3 directly cleaves procaspase-6 in recombinant assays, supporting an activation route in the studied hepatocyte context. Combined CASP3/7 inhibition attenuates procaspase-6 cleavage in TNF-alpha/cycloheximide-treated primary hepatocytes but does not resolve the individual cellular contribution. AMPK-dependent procaspase-6 phosphorylation constrains this route; it is not a universal obligatory order of executioner activation.

Context

recombinant procaspase-6 cleavage and AMPK-sensitive hepatocyte death context

PMID:32029622

Figure 6A directly assays cleavage by CASP3; Figure 6B and the AMPK experiments qualify the physiological activation interpretation.

casp7_proteolysis -> casp6_proteolysis Positively Regulates

CASP7 directly cleaves procaspase-6 in recombinant assays, supporting an activation route in the studied hepatocyte context. Combined CASP3/7 inhibition attenuates procaspase-6 cleavage in TNF-alpha/cycloheximide-treated primary hepatocytes but does not resolve the individual cellular contribution. AMPK-dependent procaspase-6 phosphorylation constrains this route; it is not a universal obligatory order of executioner activation.

Context

recombinant procaspase-6 cleavage and AMPK-sensitive hepatocyte death context

PMID:32029622

Figure 6A directly assays cleavage by CASP7; Figure 6B and the AMPK experiments qualify the physiological activation interpretation.

Part 1: Principal executioner proteolysis

Neither CASP3 nor CASP7 is individually required across the represented implementations. Their disjunction is required; optional regulators or a contextual nuclear branch alone do not constitute this caspase-mediated execution module.

CASP3 or CASP7 executioner contributionRegulatory Stepexecutioner_caspase_proteolysis

This template requires at least one represented principal executioner contribution from CASP3 or CASP7. The alternatives delimit the modeled caspase-mediated execution route; they do not assert equivalent substrate repertoires or that either protease alone suffices for every apoptotic phenotype. CASP6 and nuclear remodeling remain contextual branches.

Variant set: One or both principal executioner contributions by executioner caspase (One Or More)

CASP3 executioner proteolysisRegulatory Stepcasp3_proteolysis

Activated CASP3 cleaves a broad but defined substrate repertoire, including ICAD. It is not interchangeable with CASP7 on all protein substrates and is not the only possible execution route.

Annotons

CASP3 principal executioner caspase

casp3_executioner

Participant: Family: caspase-3 subfamily

Family:

caspase-3 subfamilyPANTHER:PTHR10454:SF198 Verified human/mouse UniProt classification and official PANTHER subfamily label; biochemical assertions are restricted to the assayed representatives and contexts.

Representative Members: CASP3 (human)UniProtKB:P42574 Casp3 (mouse)UniProtKB:P70677

Function

cysteine-type endopeptidase activityGO:0004197

Processes

execution phase of apoptosisGO:0097194

Locations

cytosolGO:0005829

Activated CASP3 cleaves a broad but defined substrate repertoire, including ICAD. It is not interchangeable with CASP7 on all protein substrates and is not the only possible execution route.

PMID:18723680

Purified CASP3 and CASP7 differ in protein-substrate cleavage despite similar synthetic-peptide activity.

PMID:9108473

Caspase-3 cleaves the DFF45 inhibitor and releases a DNA-fragmenting factor.

CASP7 substrate-selective proteolysisRegulatory Stepcasp7_proteolysis

CASP7 cleaves selected apoptotic substrates including PARP1 and p23. Its overlapping substrate repertoire with CASP3 is not identical; contributions depend on cell and genetic context.

Annotons

CASP7 executioner caspase

casp7_executioner

Participant: Family: caspase-7 subfamily

Family:

caspase-7 subfamilyPANTHER:PTHR10454:SF31 Verified human/mouse UniProt classification and official PANTHER subfamily label; biochemical assertions are restricted to the assayed representatives and contexts.

Representative Members: CASP7 (human)UniProtKB:P55210 Casp7 (mouse)UniProtKB:P97864

Function

cysteine-type endopeptidase activityGO:0004197

Processes

execution phase of apoptosisGO:0097194

Locations

cytosolGO:0005829 nucleusGO:0005634

CASP7 cleaves selected apoptotic substrates including PARP1 and p23. Its overlapping substrate repertoire with CASP3 is not identical; contributions depend on cell and genetic context.

PMID:18723680

Biochemical comparison distinguishes CASP7 substrate preferences from CASP3.

PMID:38824481

Mouse genetic studies contextualize redundancy, strain effects and non-apoptotic roles.

PMID:15525783

Mouse CASP7 efficiently cleaves ICAD in the reported comparison, unlike human CASP7; strain-dependent expression and activation correlate with DNA fragmentation in Casp3-null precursor neurons.

Part 2: Context-dependent CASP6 proteolysis (optional)

Context-dependent CASP6 proteolysisRegulatory Stepcasp6_proteolysis

CASP6 contributes distinct proteolysis, exemplified by lamin A cleavage. Its activation routes and tissue requirements differ from CASP3/CASP7; this node does not assert a universal initiator-to-CASP6 relay or XIAP inhibition.

Annotons

CASP6 executioner and amplifier caspase

casp6_executioner

Participant: Family: caspase-6 subfamily

Family:

caspase-6 subfamilyPANTHER:PTHR10454:SF206 Verified human/mouse UniProt classification and official PANTHER subfamily label; biochemical assertions are restricted to the assayed representatives and contexts.

Representative Members: CASP6 (human)UniProtKB:P55212 Casp6 (mouse)UniProtKB:O08738

Function

cysteine-type endopeptidase activityGO:0004197

Processes

execution phase of apoptosisGO:0097194

Locations

cytosolGO:0005829 nucleoplasmGO:0005654

PMID:8663580

Mch2/CASP6 is processed to an active protease during apoptosis and cleaves lamin A.

PMID:38824481

Mouse caspase studies reveal contextual and non-apoptotic functions rather than an obligatory equivalent executioner role.

PMID:32029622

Recombinant CASP3 and CASP7 each cleave procaspase-6. Primary-hepatocyte inhibitor experiments and AMPK-sensitive cleavage support a contextual activation route, not a universal caspase hierarchy.

Part 3: XIAP restraint of active CASP3/CASP7 (optional)

XIAP restraint of active CASP3/CASP7Regulatory Stepiap_caspase_restraint

The linker preceding XIAP BIR2 blocks active CASP3/CASP7 substrate-binding clefts, with BIR2 contributing regulatory interactions. BIR3 restraint of initiator CASP9 is outside the downstream boundary. BIR-domain membership alone does not establish this inhibitory function.

Annotons

XIAP caspase inhibitor

xiap_caspase_inhibitor

Participant: Family: XIAP subfamily

Family:

XIAP subfamilyPANTHER:PTHR10044:SF115 Verified human/mouse UniProt classification and official PANTHER subfamily label; biochemical assertions are restricted to the assayed representatives and contexts.

Representative Members: XIAP (human)UniProtKB:P98170 Xiap (mouse)UniProtKB:Q60989

Function

cysteine-type endopeptidase inhibitor activityGO:0004869

Processes

negative regulation of apoptotic processGO:0043066

Locations

cytosolGO:0005829

PMID:11257232

Human CASP3-XIAP structure shows a substrate-cleft steric blockade by the N-terminal extension of BIR2.

PMID:11257231

Human CASP7-XIAP structure and biochemical tests distinguish the inhibitory linker from BIR2 regulation.

PMID:19626005

Native mouse XIAP controls the mitochondrial amplification requirement in type-II FAS signaling.

Part 4: Mitochondrial SMAC/DIABLO antagonism (optional)

Mitochondrial SMAC/DIABLO antagonismRegulatory Stepmitochondrial_iap_antagonism

Processed SMAC/DIABLO binds XIAP BIR surfaces and can relieve inhibition. Antagonism depends on inhibitor architecture, stoichiometry and cell state; endogenous mitochondrial release is not universally sufficient.

Annotons

DIABLO/SMAC IAP antagonist

diablo_iap_antagonist

Participant: Family: SMAC/DIABLO subfamily

Family:

SMAC/DIABLO subfamilyPANTHER:PTHR32247:SF3 Verified human/mouse UniProt classification and official PANTHER subfamily label; biochemical assertions are restricted to the assayed representatives and contexts.

Representative Members: DIABLO (human)UniProtKB:Q9NR28 Diablo (mouse)UniProtKB:Q9JIQ3

Function

BIR domain bindingGO:1990525

Targets: XIAP BIR-domain surfaces

Processes

intrinsic apoptotic signaling pathwayGO:0097193

Locations

cytosolGO:0005829

PMID:10929712

Processed DIABLO binds IAP proteins and counteracts MIHA/XIAP-mediated protection in the tested cells.

PMID:14512414

Efficient relief of XIAP inhibition requires its linked BIR2/BIR3 architecture in the tested biochemical system.

PMID:14623868

Endogenous SMAC release does not overcome XIAP restraint in the tested sympathetic neurons.

Part 5: ICAD-dependent CAD folding (optional)

The ICAD/CAD branch is optional relative to overall apoptotic death. Within the represented CAD route, productive ICAD-assisted folding and relief of ICAD inhibition remain prerequisites for nuclease activity; optional does not remove these dependencies.

ICAD-dependent CAD foldingRegulatory Stepcad_folding

ICAD/DFFA supports productive folding of CAD before remaining associated as an inhibitor. Folding and inhibition are distinct activities; the C-terminal region required for chaperoning is not equivalently required for inhibition.

Annotons

DFFA CAD-folding chaperone

dffa_cad_chaperone

Participant: Family: ICAD/DFFA subfamily

Family:

ICAD/DFFA subfamilyPANTHER:PTHR12306:SF16 Verified human/mouse UniProt classification and official PANTHER subfamily label; biochemical assertions are restricted to the assayed representatives and contexts.

Representative Members: DFFA (human)UniProtKB:O00273 Dffa (mouse)UniProtKB:O54786

Function

protein folding chaperoneGO:0044183

Targets: DFFB/CAD

Processes

protein foldingGO:0006457

Locations

cytosolGO:0005829

PMID:9671700

Recombinant active DFF requires coexpression of DFF40 and DFF45.

PMID:19944011

C-terminal DFF45 structural requirements distinguish chaperone activity from DFF40 inhibition.

PMID:24890510

Review integrates biochemical folding and native CAD/ICAD-null phenotypes.

PMID:9422506

Mouse lymphoma CAD/ICAD discovery and recombinant coexpression establish the chaperone/inhibitor arrangement; the original import model is not imposed on all cells.

PMID:10336474

ICAD-L supported functional CAD production in the reported cell-free synthesis and coexpression assays; this does not establish that every ICAD isoform has equivalent folding activity.

PMID:9770511

Native mouse Dffa disruption abolishes extract DNA-fragmentation activity and impairs nuclear changes in tested immune cells. This necessity phenotype corroborates the functional complex, not DNase catalysis by DFFA.

Part 6: ICAD inhibition of CAD nuclease (optional)

ICAD inhibition of CAD nucleaseRegulatory Stepcad_inhibition

Intact ICAD/DFFA inhibits CAD catalysis without necessarily preventing DNA binding. Caspase cleavage dismantles this inhibition. Nuclear and cytosolic pools are context dependent, rather than requiring a universal post-cleavage import step.

Annotons

DFFA/ICAD DNase inhibitor

dffa_icad_inhibitor_chaperone

Participant: Family: ICAD/DFFA subfamily

Family:

Representative Members: DFFA (human)UniProtKB:O00273 Dffa (mouse)UniProtKB:O54786

Function

deoxyribonuclease inhibitor activityGO:0060703

Targets: DFFB/CAD

Processes

negative regulation of apoptotic DNA fragmentationGO:1902511

Locations

cytosolGO:0005829 nucleoplasmGO:0005654

PMID:15572351

The DFF complex binds DNA while ICAD inhibits DNA cleavage; activation can occur in a DNA-bound state.

PMID:9108473

Caspase-3 cleavage of DFF45 releases DNA fragmentation without a further caspase-3 requirement.

PMID:9422506

Recombinant ICAD inhibits mouse CAD DNase activity and nuclear DNA degradation.

Part 7: CAD chromatin DNA cleavage (optional)

CAD chromatin DNA cleavageRegulatory Stepdff_dna_fragmentation

Activated CAD/DFFB cleaves chromatin DNA and can promote condensation in defined systems. Oligonucleosomal fragmentation and apoptotic nuclear morphology can be uncoupled; neither is an invariant readout of all cell death.

Annotons

DFFB/CAD apoptotic DNase

dffb_cad_dnase

Participant: Family: CAD/DFFB subfamily

Family:

CAD/DFFB subfamilyPANTHER:PTHR13067:SF2 Verified human/mouse UniProt classification and official PANTHER subfamily label; biochemical assertions are restricted to the assayed representatives and contexts.

Representative Members: DFFB (human)UniProtKB:O76075 Dffb (mouse)UniProtKB:O54788

Function

DNA endonuclease activityGO:0004520

Processes

apoptotic DNA fragmentationGO:0006309

Locations

nucleoplasmGO:0005654 chromatinGO:0000785

PMID:9671700

Purified DFF40 has intrinsic nuclease activity and can trigger condensation in isolated nuclei.

PMID:9689044

Cloned human CAD has inhibitor-dependent folding and supports apoptotic DNA fragmentation.

PMID:22253444

Human neuroblastoma lines differ in cytosolic CAD availability and DNA laddering despite apoptotic nuclear morphology.

PMID:9422506

CAD identified from mouse lymphoma cells provides a direct mouse biochemical anchor alongside the human studies.

PMID:9422513

ICAD-expressing human Jurkat transfectants can resist DNA degradation while staurosporine still kills the cells; CAD-dependent laddering is not synonymous with cell death. Interpret alongside the published correction PMID:26416741.

Part 8: Contextual Acinus nuclear remodeling (optional)

Contextual Acinus nuclear remodelingRegulatory Stepacinus_remodeling

Cleaved Acinus promotes condensation in the original cell-free assay and in certain regulated experimental contexts. Other RNA-interference experiments preserve condensation while impairing DNA laddering. Its separate RNA-processing function does not identify the molecular mechanism of this contextual nuclear-remodeling activity.

Context

Homo sapiensNCBITaxon:9606

Annotons

ACIN1 apoptotic chromatin condensation factor

acin1_chromatin_condensation

Participant: Family: Acinus subfamily

Family:

Acinus subfamilyPANTHER:PTHR46589:SF1 Verified human UniProt classification and official PANTHER label. The human experimental activity is not asserted for every family member.

Representative Members: ACIN1 (human)UniProtKB:Q9UKV3

Function

caspase-activated chromatin-condensation-promoting activity Contextual experimental effector role; the precise molecular activity is unresolved and is not equated with RNA binding.

Processes

apoptotic chromosome condensationGO:0030263

Locations

nucleusGO:0005634 nucleoplasmGO:0005654

PMID:10490026

Original reconstitution identifies a CASP3-activated Acinus fragment capable of promoting condensation.

PMID:16537548

Acinus knockdown does not inhibit condensation in the tested intact-cell/cell-free systems but impairs DNA fragmentation.

PMID:16177823

Akt-dependent Acinus regulation provides an additional tested context for cleavage and condensation.

Part 9: Contextual AIF chromatin engagement (optional)

Contextual AIF chromatin engagementRegulatory Stepaif_chromatin_engagement

Processed nuclear AIFM1 can bind DNA and contribute to nuclear changes in stimulus-dependent cell death. Direct human-protein DNA binding supports this activity; the functional experiments also use rodent cells. The apoptotic PARP1-fragment route is distinct from PARP1/MIF parthanatos, cited as a boundary comparison rather than as an apoptotic-process assertion. Neither a universal CASP3-to-AIF edge nor intrinsic AIF nuclease activity is inferred.

Context

Homo sapiensNCBITaxon:9606

Annotons

AIFM1 pro-apoptotic chromatin engagement

aifm1_chromatin_engagement

Participant: Family: AIFM1 subfamily

Family:

AIFM1 subfamilyPANTHER:PTHR43557:SF4 Verified human UniProt classification and official PANTHER label. The human experimental activity is not asserted for every family member.

Representative Members: AIFM1 (human)UniProtKB:O95831

Function

DNA bindingGO:0003677

Processes

positive regulation of apoptotic processGO:0043065

Locations

nucleusGO:0005634

PMID:12198487

Recombinant human AIF binds DNA; DNA-binding-defective mutants lose apoptogenic activity while retaining nuclear translocation in the tested cellular assays. Binding, not intrinsic nuclease chemistry, is established.

PMID:9989411

Recombinant AIF causes nuclear changes that resist the tested caspase inhibitor.

PMID:27846469

Boundary comparison: AIF recruits MIF nuclease in PARP1-driven parthanatos. This source does not make parthanatos an apoptotic process or assign nuclease activity to AIF.

PMID:33168626

In staurosporine- or actinomycin-D-treated HeLa cells, a caspase-generated PAR-bearing 89-kDa PARP1 fragment facilitates AIF nuclear redistribution; this stimulus-specific mechanism is not universally caspase independent.