---
id: P99999
gene_symbol: CYCS
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  CYCS encodes human cytochrome c, a small (105 aa, ~12 kDa) soluble heme-containing
  electron carrier protein of the mitochondrial intermembrane space. Cytochrome c
  has two
  well-established, evolutionarily conserved functions: (1) In the mitochondrial electron
  transport chain, it shuttles single electrons from Complex III (cytochrome bc1,
  via its
  cytochrome c1 subunit) to Complex IV (cytochrome c oxidase), accepting electrons
  via its
  covalently bound heme c group. (2) In apoptosis, upon mitochondrial outer membrane
  permeabilization (MOMP) triggered by pro-apoptotic Bcl-2 family members (BAX/BAK),
  cytochrome c is released into the cytosol where it binds Apaf-1 to form the apoptosome,
  activating caspase-9 and triggering the downstream caspase cascade. The heme c prosthetic
  group is covalently attached via thioether bonds to Cys14 and Cys17 (mature numbering
  Cys15 and Cys18 in UniProt), with His18 and Met80 as axial ligands to the iron atom.
  Gain-of-function mutations in CYCS (e.g., G42S) cause thrombocytopenia type 4 (THC4)
  by
  enhancing apoptotic activation in the megakaryocyte/platelet lineage. Cytochrome
  c is
  one of the most extensively studied proteins in biochemistry and a classic example
  of a
  dual-function (moonlighting) protein.
existing_annotations:
# ============================================================
# IBA ANNOTATIONS (phylogenetic inference from GO_Central)
# ============================================================
  - term:
      id: GO:0009055
      label: electron transfer activity
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        IBA annotation for electron transfer activity. Cytochrome c is the canonical
        single-electron
        carrier of the mitochondrial ETC, shuttling electrons from Complex III to
        Complex
        IV via
        reversible oxidation/reduction of its heme c iron atom. This is one of the
        two
        core molecular
        functions of CYCS and is extremely well established. The IBA annotation is
        phylogenetically
        sound as this function is conserved across all eukaryotes (PMID:9515723).
      action: ACCEPT
      reason: >-
        Electron transfer activity is the primary molecular function of cytochrome
        c
        in the
        respiratory chain. The protein shuttles single electrons between Complex III
        and Complex IV.
        This function is conserved across eukaryotes and is phylogenetically well
        supported
        by the IBA.
      supported_by:
        - reference_id: PMID:9515723
          supporting_text: >-
            cytochrome c is a pro-apoptotic factor. It is released from its places
            on
            the outer
            surface of the inner mitochondrial membrane at early steps of apoptosis
        - reference_id: file:human/CYCS/CYCS-deep-research-falcon.md
          supporting_text: >-
            cytochrome c shuttles electrons from complex III (cytochrome bc1) to complex
            IV
            (cytochrome c oxidase) in the inner mitochondrial membrane cristae region,
            supporting
            oxidative phosphorylation
  - term:
      id: GO:0006122
      label: mitochondrial electron transport, ubiquinol to cytochrome c
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        IBA annotation for the biological process of electron transfer from ubiquinol
        to cytochrome c.
        This represents the Complex III (cytochrome bc1) reaction in which ubiquinol
        is oxidized and
        cytochrome c is reduced. Cytochrome c is the electron acceptor in this reaction,
        receiving
        electrons from the cytochrome c1 subunit of Complex III. While CYCS is not
        a
        subunit of
        Complex III, it is an essential participant in this process as the mobile
        electron
        carrier
        that accepts the electrons. The IBA annotation is appropriate as this function
        is conserved
        across eukaryotes.
      action: ACCEPT
      reason: >-
        Cytochrome c is the direct electron acceptor from Complex III. The process
        of
        ubiquinol-to-
        cytochrome c electron transfer requires cytochrome c as the mobile carrier.
        This is a core
        biological process annotation that accurately describes one half of CYCS's
        ETC
        function.
      supported_by:
        - reference_id: file:human/CYCS/CYCS-deep-research-falcon.md
          supporting_text: >-
            cytochrome c shuttles electrons from complex III (cytochrome bc1) to complex
            IV
            (cytochrome c oxidase)
  - term:
      id: GO:0005758
      label: mitochondrial intermembrane space
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        IBA annotation for mitochondrial intermembrane space localization. Cytochrome
        c resides in
        the IMS, loosely associated with the inner membrane via electrostatic and
        hydrophobic
        interactions including cardiolipin binding. This is the site of its electron
        transfer
        function and is conserved across eukaryotes. UniProt confirms this localization:
        "Mitochondrion
        intermembrane space. Loosely associated with the inner membrane." The IBA
        is
        phylogenetically
        appropriate.
      action: ACCEPT
      reason: >-
        Mitochondrial intermembrane space is the primary localization of cytochrome
        c during its
        electron transfer function. This is a core CC annotation, well established
        experimentally
        and phylogenetically sound.
      supported_by:
        - reference_id: PMID:9515723
          supporting_text: >-
            It is released from its places on the outer surface of the inner mitochondrial
            membrane
  - term:
      id: GO:0006123
      label: mitochondrial electron transport, cytochrome c to oxygen
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        IBA annotation for the biological process of electron transfer from cytochrome
        c to oxygen.
        This represents the Complex IV (cytochrome c oxidase) reaction where cytochrome
        c donates
        electrons and molecular oxygen is reduced to water. Cytochrome c is the electron
        donor in
        this reaction. As with GO:0006122, CYCS is not a subunit of Complex IV but
        is
        an essential
        participant as the electron donor. The IBA annotation is appropriate.
      action: ACCEPT
      reason: >-
        Cytochrome c is the direct electron donor to Complex IV. This process requires
        cytochrome c
        as the mobile carrier that delivers electrons from Complex III. This is a
        core
        biological
        process annotation for CYCS.
      supported_by:
        - reference_id: file:human/CYCS/CYCS-deep-research-falcon.md
          supporting_text: >-
            cytochrome c shuttles electrons from complex III (cytochrome bc1) to complex
            IV
            (cytochrome c oxidase) in the inner mitochondrial membrane cristae region

# ============================================================
# IEA ANNOTATIONS (electronic/computational)
# ============================================================
  - term:
      id: GO:0005758
      label: mitochondrial intermembrane space
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: >-
        IEA annotation for mitochondrial intermembrane space based on UniProt subcellular
        location
        mapping. Consistent with the IBA annotation for the same term and with direct
        experimental
        evidence (IDA from PMID:19393246). Redundant but correct.
      action: ACCEPT
      reason: >-
        Correct and consistent with IBA and IDA annotations for the same term. IEA
        mapping
        from
        UniProt subcellular location is accurate for this well-characterized localization.
  - term:
      id: GO:0006915
      label: apoptotic process
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >-
        IEA annotation for apoptotic process from UniProt keyword mapping (KW-0053,
        Apoptosis).
        Cytochrome c is indeed involved in apoptosis -- upon release from mitochondria
        it triggers
        the intrinsic apoptotic pathway. However, GO:0006915 (apoptotic process) is
        very broad.
        More specific terms such as GO:0097193 (intrinsic apoptotic signaling pathway)
        are also
        annotated. This broad IEA is acceptable alongside the more specific annotations.
      action: ACCEPT
      reason: >-
        Correct but broad. The role of cytochrome c in apoptosis is well established
        (PMID:8689682,
        PMID:9267021, PMID:10206961). More specific child terms are also annotated.
        It is acceptable
        for IEA annotations to use broader terms.
  - term:
      id: GO:0009055
      label: electron transfer activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: >-
        IEA annotation for electron transfer activity from InterPro domain mapping
        (IPR002327,
        IPR009056, IPR036909). The cytochrome c domain is a well-characterized electron
        transfer
        domain. Consistent with the IBA annotation for the same term.
      action: ACCEPT
      reason: >-
        Correct and consistent with the IBA annotation. The cytochrome c domain family
        is defined
        by its electron transfer function.
  - term:
      id: GO:0020037
      label: heme binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: >-
        IEA annotation for heme binding from InterPro domain mapping. Cytochrome c
        contains
        a
        covalently bound heme c group attached via thioether bonds to Cys15 and Cys18
        (PMID:23150584
        per UniProt). This is a core structural feature essential for both electron
        transfer and
        the protein's redox properties. Consistent with the TAS annotation from PMID:9515723.
      action: ACCEPT
      reason: >-
        Heme binding is a core molecular function of cytochrome c. The heme c group
        is covalently
        attached and is essential for electron transfer activity.
  - term:
      id: GO:0022904
      label: respiratory electron transport chain
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >-
        IEA annotation for respiratory electron transport chain from UniProt keyword
        mapping
        (KW-0679, Respiratory chain). This is broader than the specific IBA annotations
        for
        GO:0006122 and GO:0006123 but is correct. Cytochrome c is a key component
        of
        the
        respiratory electron transport chain.
      action: ACCEPT
      reason: >-
        Correct but general. The specific IBA annotations for Complex III-to-cyt c
        and
        cyt c-to-O2
        processes are more informative, but this broader term is acceptable for IEA.
  - term:
      id: GO:0046872
      label: metal ion binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >-
        IEA annotation for metal ion binding from UniProt keyword mapping (KW-0479,
        Metal-binding).
        Cytochrome c contains a heme iron atom coordinated by His18 and Met80 (axial
        ligands).
        While technically correct, GO:0046872 is very broad. The more informative
        annotation
        is
        GO:0020037 (heme binding) which captures the specific nature of the metal
        coordination
        context. However, iron ion binding is part of the heme function and this IEA
        is not wrong.
      action: ACCEPT
      reason: >-
        Technically correct -- cytochrome c binds iron as part of its heme prosthetic
        group. The
        more specific GO:0020037 (heme binding) is also annotated. It is acceptable
        for IEA
        annotations to use broader terms.

# ============================================================
# IPI ANNOTATIONS (protein-protein interaction - protein binding)
# ============================================================
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:10206961
    review:
      summary: >-
        IPI annotation for protein binding with APAF1 (O14727) from Zou et al. 1999.
        This study
        reconstituted the apoptosome using purified cytochrome c, recombinant APAF-1,
        and recombinant
        procaspase-9, demonstrating direct physical interaction between cytochrome
        c
        and APAF-1
        (PMID:10206961). This is one of the most biologically significant interactions
        of CYCS --
        cytochrome c binding to Apaf-1 triggers apoptosome assembly and caspase-9
        activation.
        While
        'protein binding' is uninformative, the underlying interaction is a core function.
        A more
        informative term would be GO:0008656 (cysteine-type endopeptidase activator
        activity involved
        in apoptotic process) but that does not fully capture the binding aspect.
      action: KEEP_AS_NON_CORE
      reason: >-
        The CYCS-APAF1 interaction is among the most biologically significant known
        protein-protein
        interactions, as it initiates apoptosome assembly. However, 'protein binding'
        is too vague
        to be informative. The functional significance is better captured by the BP
        annotation
        GO:0097193 (intrinsic apoptotic signaling pathway) and the CC annotation for
        apoptosome.
      supported_by:
        - reference_id: PMID:10206961
          supporting_text: >-
            the binding of cytochrome c promote APAF-1 oligomerization, forming a
            large
            multimeric
            APAF-1.cytochrome c complex
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:25416956
    review:
      summary: >-
        IPI annotation for protein binding with KRT40 (Q6A162) from a proteome-scale
        human
        interactome study (Rolland et al. 2014). KRT40 is a keratin family member.
        The
        biological
        relevance of a CYCS-KRT40 interaction is unclear and likely represents a non-specific
        high-throughput detection.
      action: KEEP_AS_NON_CORE
      reason: >-
        High-throughput interactome study. The CYCS-KRT40 interaction has no established
        biological
        significance. 'Protein binding' is uninformative.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:25595453
    review:
      summary: >-
        IPI annotation for protein binding with plant cytochrome c1 (Q9FKS5) from
        Moreno-Beltran
        et al. 2015. This study investigated the transient interactions of human cytochrome
        c
        with respiratory complexes III and IV using cross-species proteins. The study
        showed that
        two molecules of cytochrome c can bind to each complex at low ionic strength,
        supporting
        the electron transfer shuttle function (PMID:25595453). This is a functionally
        relevant
        interaction, though with a heterologous system.
      action: KEEP_AS_NON_CORE
      reason: >-
        Heterologous system study (human cyt c with plant cyt c1). Demonstrates the
        conserved
        interaction between cytochrome c and its respiratory chain partners. 'Protein
        binding' is
        uninformative but the underlying biology is sound.
      supported_by:
        - reference_id: PMID:25595453
          supporting_text: >-
            two cytochrome c molecules per adduct - at low ionic strength. We conclude
            that such
            extra binding sites at the surfaces of complexes III and IV can facilitate
            the turnover
            and sliding of cytochrome c molecules
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:25910212
    review:
      summary: >-
        IPI annotation for protein binding with KRT40 (Q6A162) from Sahni et al. 2015,
        a study
        on macromolecular interaction perturbations in human genetic disorders. Second
        detection of
        CYCS-KRT40 interaction. Biological significance remains unclear.
      action: KEEP_AS_NON_CORE
      reason: >-
        High-throughput interaction study. Repeated CYCS-KRT40 detection but no established
        biological significance.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:28514442
    review:
      summary: >-
        IPI annotation for protein binding with LRG1 (P02750) from Huttlin et al.
        2017,
        the
        architecture of the human interactome study. LRG1 is a leucine-rich alpha-2-glycoprotein
        involved in TGF-beta signaling. The biological relevance of this interaction
        is unclear.
      action: KEEP_AS_NON_CORE
      reason: >-
        High-throughput interactome study. CYCS-LRG1 interaction has no established
        biological
        significance. 'Protein binding' is uninformative.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:32296183
    review:
      summary: >-
        IPI annotation for protein binding with MEOX2 (Q6FHY5) from Luck et al. 2020,
        a reference
        map of the human binary protein interactome. MEOX2 is a homeobox transcription
        factor.
        The biological relevance of this interaction is unclear.
      action: KEEP_AS_NON_CORE
      reason: >-
        High-throughput interactome study. CYCS-MEOX2 interaction has no established
        biological
        significance. 'Protein binding' is uninformative.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:32814053
    review:
      summary: >-
        IPI annotation for protein binding from Haenig et al. 2020, an interactome
        mapping
        study
        focused on neurodegenerative disease proteins. This PMID generates multiple
        GOA entries
        with different interactors including APP (P05067), SNCA (P37840), FYN (P06241),
        COA7
        (Q96BR5), and many others. The APP and SNCA interactions are biologically
        interesting
        given that cytochrome c release and caspase activation are implicated in neurodegeneration.
        However, most of these are high-throughput detections and 'protein binding'
        is uninformative.
      action: KEEP_AS_NON_CORE
      reason: >-
        Large-scale neurodegenerative disease interactome study with many interactors.
        Some
        interactions (APP, SNCA) are potentially biologically interesting but the
        evidence
        is from
        high-throughput screening. 'Protein binding' is uninformative.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:33961781
    review:
      summary: >-
        IPI annotation for protein binding with LRG1 (P02750) from Huttlin et al.
        2021,
        dual
        proteome-scale networks study. Second detection of CYCS-LRG1 interaction.
      action: KEEP_AS_NON_CORE
      reason: >-
        High-throughput interactome study. Repeated CYCS-LRG1 detection but no established
        biological significance.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:9267021
    review:
      summary: >-
        IPI annotation for protein binding with APAF1 (O14727) from Zou et al. 1997.
        This is the
        landmark paper identifying Apaf-1 as the cytochrome c-binding partner that
        mediates
        caspase activation. The study showed that "Cytochrome c binds to Apaf-1, an
        event that may
        trigger the activation of caspase-3, leading to apoptosis" (PMID:9267021).
        This
        is one of the
        most important protein interactions discovered for CYCS.
      action: KEEP_AS_NON_CORE
      reason: >-
        Landmark paper establishing the CYCS-APAF1 interaction. The biological significance
        is
        enormous but 'protein binding' is uninformative. The functional context is
        captured
        by
        GO:0097193 and GO:0097194 annotations.
      supported_by:
        - reference_id: PMID:9267021
          supporting_text: >-
            Cytochrome c binds to Apaf-1, an event that may trigger the activation
            of
            caspase-3,
            leading to apoptosis

# ============================================================
# LOCALIZATION ANNOTATIONS - MITOCHONDRION
# ============================================================
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: IDA
    original_reference_id: GO_REF:0000052
    review:
      summary: >-
        IDA annotation for mitochondrial localization from HPA immunofluorescence
        data
        curation.
        Cytochrome c is a well-established mitochondrial protein. The mitochondrial
        intermembrane
        space (GO:0005758) is the more specific localization, but the broader mitochondrion
        annotation is also correct.
      action: ACCEPT
      reason: >-
        Correct localization supported by immunofluorescence. A broader term than
        GO:0005758
        but
        still accurate.

# ============================================================
# APOPTOSIS PATHWAY ANNOTATIONS
# ============================================================
  - term:
      id: GO:0097193
      label: intrinsic apoptotic signaling pathway
    evidence_type: NAS
    original_reference_id: PMID:10206961
    review:
      summary: >-
        NAS annotation from ComplexPortal for the intrinsic apoptotic signaling pathway.
        Zou et al.
        1999 (PMID:10206961) reconstituted the apoptosome from purified cytochrome
        c,
        APAF-1, and
        procaspase-9, directly demonstrating that cytochrome c is a key activator
        of
        the intrinsic
        apoptotic pathway. This is a core biological process for CYCS.
      action: ACCEPT
      reason: >-
        The intrinsic apoptotic signaling pathway is one of the two core biological
        processes for
        CYCS. Cytochrome c triggers apoptosome assembly by binding APAF-1, which leads
        to caspase-9
        activation. This is extensively supported by multiple landmark studies.
      supported_by:
        - reference_id: PMID:10206961
          supporting_text: >-
            the binding of cytochrome c promote APAF-1 oligomerization, forming a
            large
            multimeric
            APAF-1.cytochrome c complex. Such a complex can be isolated using gel
            filtration
            chromatography and is by itself sufficient to recruit and activate procaspase-9
  - term:
      id: GO:0097190
      label: apoptotic signaling pathway
    evidence_type: ISS
    original_reference_id: PMID:12107093
    review:
      summary: >-
        ISS annotation for apoptotic signaling pathway, inferred from mouse ortholog
        (UniProtKB:P00004).
        Roberg et al. 2002 (PMID:12107093) showed that cathepsin D injection causes
        apoptosis with
        cytochrome c redistribution and caspase activation. The ISS from mouse is
        appropriate
        since
        the apoptotic function of cytochrome c is conserved across mammals. However,
        this is a
        broader term than GO:0097193 (intrinsic apoptotic signaling pathway) which
        is
        already
        annotated. Both are acceptable.
      action: ACCEPT
      reason: >-
        Correct but broader than GO:0097193. The apoptotic signaling function of cytochrome
        c
        is conserved in mouse, making the ISS transfer appropriate.
      supported_by:
        - reference_id: PMID:12107093
          supporting_text: >-
            microinjection of cathepsin D into the cytosol of human fibroblasts caused
            apoptosis,
            which was detected as changes in distribution of cytochrome c, cell shrinkage,
            activation of caspases
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: HTP
    original_reference_id: PMID:34800366
    review:
      summary: >-
        HTP annotation for mitochondrial localization from Morgenstern et al. 2021,
        a quantitative
        high-confidence human mitochondrial proteome study. Cytochrome c was identified
        in the
        mitochondrial proteome. Correct but less specific than GO:0005758.
      action: ACCEPT
      reason: >-
        Correct. Cytochrome c is a well-established mitochondrial protein. Confirmed
        by this
        high-confidence proteomics study.

# ============================================================
# LOCALIZATION ANNOTATIONS - MITOCHONDRIAL INNER MEMBRANE (Reactome)
# ============================================================
  - term:
      id: GO:0005743
      label: mitochondrial inner membrane
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-163214
    review:
      summary: >-
        TAS annotation from Reactome pathway R-HSA-163214 (Electron transfer from
        reduced
        cytochrome c to molecular oxygen). Cytochrome c is associated with the inner
        mitochondrial
        membrane in the intermembrane space, where it interacts with Complex III and
        Complex IV
        embedded in the inner membrane. However, cytochrome c is a soluble protein
        of
        the IMS, not
        an integral or peripheral inner membrane protein. GO:0005758 (mitochondrial
        intermembrane
        space) is more accurate than GO:0005743. That said, UniProt notes cytochrome
        c is "Loosely
        associated with the inner membrane" via electrostatic and cardiolipin interactions,
        so
        this annotation is not entirely wrong.
      action: ACCEPT
      reason: >-
        While GO:0005758 (mitochondrial intermembrane space) is the more precise localization,
        cytochrome c is indeed loosely associated with the inner membrane surface
        via
        cardiolipin
        binding. Reactome correctly places it in the context of inner membrane electron
        transport.
      supported_by:
        - reference_id: file:human/CYCS/CYCS-deep-research-falcon.md
          supporting_text: >-
            cytochrome c is localized to the mitochondrial intermembrane space (IMS),
            associated
            with the inner mitochondrial membrane via electrostatic and hydrophobic
            interactions,
            including binding to cardiolipin-rich cristae surfaces
  - term:
      id: GO:0005743
      label: mitochondrial inner membrane
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-164651
    review:
      summary: >-
        TAS from Reactome R-HSA-164651 (Electron transfer from ubiquinol to cytochrome
        c of
        complex III). Same reasoning as above -- cytochrome c is loosely associated
        with the inner
        membrane during electron transfer.
      action: ACCEPT
      reason: >-
        Consistent with the Reactome annotation for Complex III reaction context.
        Cytochrome
        c
        is associated with the inner membrane surface during its electron carrier
        function.
  - term:
      id: GO:0005743
      label: mitochondrial inner membrane
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-3341294
    review:
      summary: >-
        TAS from Reactome R-HSA-3341294 (Superoxide reduces cytochrome c). This reaction
        occurs
        in the IMS at the inner membrane surface. Same reasoning as above.
      action: ACCEPT
      reason: >-
        Consistent with inner membrane association during superoxide scavenging by
        cytochrome
        c
        in the IMS.
  - term:
      id: GO:0005743
      label: mitochondrial inner membrane
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-9866217
    review:
      summary: >-
        TAS from Reactome R-HSA-9866217 (HCCS inserts heme into cytochrome c). HCCS
        is the
        holocytochrome c synthase that catalyzes heme attachment to apocytochrome
        c
        at the inner
        membrane. The heme insertion occurs at or near the inner membrane in the IMS.
      action: ACCEPT
      reason: >-
        Appropriate localization for the heme attachment reaction catalyzed by HCCS
        at the inner
        membrane.

# ============================================================
# APOPTOSIS EXECUTION ANNOTATIONS
# ============================================================
  - term:
      id: GO:0097194
      label: execution phase of apoptosis
    evidence_type: TAS
    original_reference_id: PMID:9267021
    review:
      summary: >-
        TAS annotation for the execution phase of apoptosis, citing Zou et al. 1997
        (PMID:9267021).
        This landmark paper identified Apaf-1 and showed that cytochrome c binding
        to
        Apaf-1
        leads to caspase-3 activation, which is the execution phase of apoptosis.
        However,
        cytochrome c's direct role is in the initiation/signaling phase (binding Apaf-1,
        activating
        caspase-9) rather than the execution phase per se (which involves effector
        caspases
        cleaving
        cellular substrates). CYCS acts upstream of execution. GO:0097193 (intrinsic
        apoptotic
        signaling pathway) is the more appropriate process term.
      action: MODIFY
      reason: >-
        Cytochrome c participates in the initiation of apoptosis by binding Apaf-1
        and
        activating
        caspase-9. The execution phase (caspase-3/7-mediated substrate cleavage) occurs
        downstream
        of cytochrome c's direct action. GO:0097193 (intrinsic apoptotic signaling
        pathway)
        more
        accurately describes CYCS's role. The existing annotation for GO:0097193 already
        captures this.
      proposed_replacement_terms:
        - id: GO:0097193
          label: intrinsic apoptotic signaling pathway
      supported_by:
        - reference_id: PMID:9267021
          supporting_text: >-
            Cytochrome c binds to Apaf-1, an event that may trigger the activation
            of
            caspase-3,
            leading to apoptosis

# ============================================================
# LOCALIZATION ANNOTATIONS - MITOCHONDRION (various evidence)
# ============================================================
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: IDA
    original_reference_id: PMID:12107093
    review:
      summary: >-
        IDA annotation for mitochondrial localization from Roberg et al. 2002 (PMID:12107093).
        This study on cathepsin D-induced apoptosis showed cytochrome c redistribution
        from
        mitochondria to cytosol, confirming its mitochondrial localization. Correct.
      action: ACCEPT
      reason: >-
        The study directly observed cytochrome c distribution, confirming mitochondrial
        localization.
      supported_by:
        - reference_id: PMID:12107093
          supporting_text: >-
            apoptosis, which was detected as changes in distribution of cytochrome
            c
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: IDA
    original_reference_id: PMID:12107093
    review:
      summary: >-
        IDA annotation for cytosol localization from Roberg et al. 2002 (PMID:12107093).
        Cytochrome c was observed in the cytosol during apoptosis, having been released
        from
        mitochondria. This is a condition-specific localization (apoptosis) rather
        than
        a
        steady-state localization. However, it is functionally significant as cytosolic
        cytochrome c triggers the intrinsic apoptotic pathway.
      action: ACCEPT
      reason: >-
        Cytosolic localization of cytochrome c is condition-specific (during apoptosis)
        but
        biologically significant. It is the site where cytochrome c exerts its apoptotic
        signaling function by binding Apaf-1.
      supported_by:
        - reference_id: PMID:12107093
          supporting_text: >-
            changes in distribution of cytochrome c, cell shrinkage, activation of
            caspases

# ============================================================
# LOCALIZATION ANNOTATIONS - MITOCHONDRIAL IMS (experimental)
# ============================================================
  - term:
      id: GO:0005758
      label: mitochondrial intermembrane space
    evidence_type: IDA
    original_reference_id: PMID:19393246
    review:
      summary: >-
        IDA annotation for mitochondrial intermembrane space from CAFA, citing Oswald
        et al. 2009
        (PMID:19393246). This study focused on COX17 knockdown and its effects on
        cytochrome
        c
        oxidase assembly and supercomplex organization. While the study's primary
        focus
        is COX17,
        it involves cytochrome c in the context of respiratory supercomplexes in the
        IMS.
        Cytochrome c IMS localization is well established independently.
      action: ACCEPT
      reason: >-
        Correct localization. The IMS is the established location of cytochrome c.
        While
        this
        particular study focuses on COX17, the IMS localization of cytochrome c is
        confirmed
        by many independent studies.
      supported_by:
        - reference_id: PMID:19393246
          supporting_text: >-
            Assembly of cytochrome c oxidase, the terminal enzyme of the mitochondrial
            respiratory
            chain, requires a concerted activity of a number of chaperones and factors
  - term:
      id: GO:0005758
      label: mitochondrial intermembrane space
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-5688294
    review:
      summary: >-
        TAS from Reactome R-HSA-5688294 (SIRT5 deacetylates Cytochrome C). This places
        cytochrome c
        in the IMS where SIRT5 deacetylation occurs. Correct localization.
      action: ACCEPT
      reason: >-
        Correct. Cytochrome c resides in the IMS and is subject to post-translational
        modifications
        including deacetylation.

# ============================================================
# LOCALIZATION ANNOTATIONS - NUCLEUS
# ============================================================
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: HDA
    original_reference_id: PMID:21630459
    review:
      summary: >-
        HDA annotation for nuclear localization from de Mateo et al. 2011 (PMID:21630459),
        a
        proteomic characterization of the human sperm nucleus. Cytochrome c was identified
        among
        403 proteins in isolated sperm nuclei. This is a high-throughput mass spectrometry
        detection
        and may represent contamination or a sperm-specific localization artifact.
        Sperm
        nuclei
        are extremely compact structures and the biological significance of cytochrome
        c in the
        nucleus is unclear and unlikely to represent a functional localization.
      action: MARK_AS_OVER_ANNOTATED
      reason: >-
        Cytochrome c is a mitochondrial IMS protein. Its detection in sperm nuclei
        by
        mass
        spectrometry is likely due to contamination from the midpiece mitochondrial
        sheath, which
        is extremely close to the sperm nucleus. There is no established functional
        role for
        cytochrome c in the nucleus. This does not represent a meaningful localization.
      supported_by:
        - reference_id: PMID:21630459
          supporting_text: >-
            sperm nuclei were obtained through CTAB treatment and isolated to over
            99.9%
            purity
            without any tail fragments, acrosome or mitochondria
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: IDA
    original_reference_id: PMID:20671748
    review:
      summary: >-
        IDA annotation for mitochondrial localization from Cleland et al. 2011 (PMID:20671748),
        a study on Bcl-2 family interaction with mitochondrial morphogenesis machinery.
        This study
        examined Bax/Bak-dependent mitochondrial dynamics and would have observed
        cytochrome
        c in
        mitochondrial contexts. Correct localization.
      action: ACCEPT
      reason: >-
        Correct. Cytochrome c is a well-established mitochondrial protein.
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: HDA
    original_reference_id: PMID:20833797
    review:
      summary: >-
        HDA annotation for mitochondrial localization from a phosphoproteome analysis
        of functional
        mitochondria isolated from resting human muscle (Zhao et al. 2011). Cytochrome
        c was
        identified in the mitochondrial proteome. Correct.
      action: ACCEPT
      reason: >-
        Correct. Cytochrome c identified in purified mitochondrial preparations by
        mass
        spectrometry.

# ============================================================
# LOCALIZATION ANNOTATIONS - MITOCHONDRIAL IMS (Reactome)
# ============================================================
  - term:
      id: GO:0005758
      label: mitochondrial intermembrane space
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-114284
    review:
      summary: >-
        TAS from Reactome R-HSA-114284 (Release of Cytochrome c from mitochondria).
        This Reactome
        entry describes the release of cytochrome c from the IMS during apoptosis.
        Correct
        localization for the starting point of the apoptotic release event.
      action: ACCEPT
      reason: >-
        Correct. Cytochrome c resides in the IMS prior to release during apoptosis.

# ============================================================
# LOCALIZATION ANNOTATIONS - CYTOSOL (Reactome, apoptosis context)
# ============================================================
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-114252
    review:
      summary: >-
        TAS from Reactome R-HSA-114252 (Cleavage of Procaspase-3 by the apoptosome).
        Cytochrome c
        is in the cytosol as part of the apoptosome during caspase-3 activation. Correct
        condition-specific localization during apoptosis.
      action: ACCEPT
      reason: >-
        Correct. Cytochrome c is in the cytosol during apoptosis as part of the apoptosome
        complex.
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-114254
    review:
      summary: >-
        TAS from Reactome R-HSA-114254 (CYCS binds to APAF1). Cytochrome c binds Apaf-1
        in the
        cytosol to initiate apoptosome formation. Correct.
      action: ACCEPT
      reason: >-
        Correct. The cytochrome c-Apaf-1 binding event occurs in the cytosol.
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-114256
    review:
      summary: >-
        TAS from Reactome R-HSA-114256 (CYCS:APAF1 binds procaspase-9). Apoptosome
        formation
        in
        the cytosol. Correct.
      action: ACCEPT
      reason: >-
        Correct. Apoptosome assembly occurs in the cytosol.
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-114259
    review:
      summary: >-
        TAS from Reactome R-HSA-114259 (Cleavage of Procaspase-9 to caspase-9). Caspase-9
        activation within the cytosolic apoptosome. Correct.
      action: ACCEPT
      reason: >-
        Correct. Caspase-9 activation occurs in the cytosol within the apoptosome.
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-114261
    review:
      summary: >-
        TAS from Reactome R-HSA-114261 (Cleavage of Procaspase-7 by the apoptosome).
        Apoptosome
        function in the cytosol. Correct.
      action: ACCEPT
      reason: >-
        Correct. Effector caspase activation by the apoptosome occurs in the cytosol.
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-114284
    review:
      summary: >-
        TAS from Reactome R-HSA-114284 (Release of Cytochrome c from mitochondria).
        This is the
        same Reactome entry used for the IMS annotation above. The cytosol annotation
        reflects
        where cytochrome c ends up after release. Correct.
      action: ACCEPT
      reason: >-
        Correct. Cytochrome c is released into the cytosol during apoptosis.
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-1592231
    review:
      summary: >-
        TAS from Reactome R-HSA-1592231 (Expression of CYCS). Cytochrome c is synthesized
        in
        the cytosol before import into mitochondria. Correct in the context of protein
        synthesis,
        though the functional localization is the IMS.
      action: ACCEPT
      reason: >-
        Correct. Cytochrome c is synthesized in the cytosol as apocytochrome c before
        mitochondrial import.
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-6804596
    review:
      summary: >-
        TAS from Reactome R-HSA-6804596 (APAF1:CYCS binds APIP). Describes APIP binding
        to the
        Apaf-1:cytochrome c complex in the cytosol. Correct.
      action: ACCEPT
      reason: >-
        Correct. This interaction occurs in the cytosol during apoptotic signaling.
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-9627056
    review:
      summary: >-
        TAS from Reactome R-HSA-9627056 (Procaspase 9 forms dimer). Dimerization of
        procaspase-9
        in the cytosol within the apoptosome context. Correct.
      action: ACCEPT
      reason: >-
        Correct. Part of the apoptosome signaling cascade in the cytosol.
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-9627078
    review:
      summary: >-
        TAS from Reactome R-HSA-9627078 (XIAP binds CASP9). Regulation of caspase-9
        by XIAP
        in the cytosol. Correct.
      action: ACCEPT
      reason: >-
        Correct. Part of the apoptosis regulatory network in the cytosol.
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-9627089
    review:
      summary: >-
        TAS from Reactome R-HSA-9627089 (CASP9 is phosphorylated at T412). Post-translational
        modification of caspase-9 in the cytosol. Correct.
      action: ACCEPT
      reason: >-
        Correct. Part of the apoptosis regulatory network in the cytosol.

# ============================================================
# NUCLEUS ANNOTATION (LIFEdb)
# ============================================================
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: IDA
    original_reference_id: GO_REF:0000054
    review:
      summary: >-
        IDA annotation from LIFEdb, based on curation of intracellular localizations
        of expressed
        fusion proteins in living cells. LIFEdb generates GFP-fusion proteins and
        observes
        their
        localization. Nuclear localization of a CYCS-GFP fusion is likely an artifact
        of the
        overexpression/fusion system. Cytochrome c is a small protein (12 kDa) that
        could
        diffuse through nuclear pores, especially when overexpressed as a GFP fusion.
        There is no
        established functional role for cytochrome c in the nucleus.
      action: MARK_AS_OVER_ANNOTATED
      reason: >-
        LIFEdb GFP-fusion protein localization. Small proteins like cytochrome c (12
        kDa) can
        passively diffuse through nuclear pores when overexpressed as fusion constructs.
        This is
        likely an artifact and does not represent a functional nuclear localization.
        The canonical
        localization of cytochrome c is the mitochondrial IMS.

# ============================================================
# HEME BINDING (TAS)
# ============================================================
  - term:
      id: GO:0020037
      label: heme binding
    evidence_type: TAS
    original_reference_id: PMID:9515723
    review:
      summary: >-
        TAS annotation for heme binding from Skulachev 1998 (PMID:9515723), a review
        on cytochrome c
        in apoptotic and antioxidant cascades. The heme c group is covalently bound
        to Cys15 and
        Cys18 via thioether bonds, with His18 and Met80 as axial iron ligands. This
        is a core
        molecular function of CYCS essential for electron transfer activity.
      action: ACCEPT
      reason: >-
        Heme binding is a defining structural and functional feature of cytochrome
        c.
        The covalent
        heme attachment is essential for its electron carrier function. Well supported
        by structural
        and biochemical evidence.
      supported_by:
        - reference_id: PMID:9515723
          supporting_text: >-
            cytochrome c is a pro-apoptotic factor. It is released from its places
            on
            the outer
            surface of the inner mitochondrial membrane

# ============================================================
# MITOCHONDRIAL IMS (TAS)
# ============================================================
  - term:
      id: GO:0005758
      label: mitochondrial intermembrane space
    evidence_type: TAS
    original_reference_id: PMID:8689682
    review:
      summary: >-
        TAS annotation for mitochondrial IMS localization from Liu et al. 1996 (PMID:8689682),
        the landmark paper demonstrating that cytochrome c is required for in vitro
        apoptosis.
        The study showed that cells undergoing apoptosis release cytochrome c from
        mitochondria
        to the cytosol, establishing its starting location in the IMS.
      action: ACCEPT
      reason: >-
        This landmark paper established the role of cytochrome c in apoptosis and
        confirmed
        its
        mitochondrial localization prior to release during apoptosis.
      supported_by:
        - reference_id: PMID:8689682
          supporting_text: >-
            Cells undergoing apoptosis in vivo showed increased release of cytochrome
            c to their
            cytosol, suggesting that mitochondria may function in apoptosis by releasing
            cytochrome c

# ============================================================
# CYTOSOL (IMP)
# ============================================================
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: IMP
    original_reference_id: PMID:8689682
    review:
      summary: >-
        IMP annotation for cytosol localization from Liu et al. 1996 (PMID:8689682).
        The study
        demonstrated that addition of cytochrome c to cytosol activates the apoptotic
        program,
        and that cells undergoing apoptosis release cytochrome c to their cytosol.
        The
        IMP
        evidence is appropriate because the mutant phenotype (apoptosis) requires
        cytochrome
        c
        presence in the cytosol.
      action: ACCEPT
      reason: >-
        Landmark experimental demonstration that cytochrome c in the cytosol activates
        apoptosis.
        The cytosolic localization is condition-specific but functionally essential
        for the
        apoptotic signaling role.
      supported_by:
        - reference_id: PMID:8689682
          supporting_text: >-
            A cell-free system based on cytosols of normally growing cells is established
            that
            reproduces aspects of the apoptotic program in vitro...protein sequence
            revealed
            that
            this protein is cytochrome c

# ============================================================
# CELLULAR RESPIRATION (TAS)
# ============================================================
  - term:
      id: GO:0045333
      label: cellular respiration
    evidence_type: TAS
    original_reference_id: PMID:10383829
    review:
      summary: >-
        TAS annotation for cellular respiration from Drosopoulos et al. 1999 (PMID:10383829).
        However, this publication is about RPTPkappa (receptor-like protein tyrosine
        phosphatase
        kappa) stimulating neurite outgrowth. It has no apparent connection to cytochrome
        c or
        cellular respiration. This reference appears to be incorrectly linked to this
        annotation.
        Nevertheless, the biological process annotation itself is correct -- cytochrome
        c is
        essential for cellular respiration as the electron carrier between Complex
        III
        and IV.
      action: ACCEPT
      reason: >-
        The GO term cellular respiration is correct for CYCS, as it is an essential
        component of
        the mitochondrial electron transport chain. The reference PMID:10383829 appears
        to be
        incorrectly linked (it is about RPTPkappa signaling, not cytochrome c), but
        the annotation
        itself is valid and supported by extensive other evidence.
      additional_reference_ids: ["PMID:9515723"]
      supported_by:
        - reference_id: PMID:9515723
          supporting_text: >-
            The reduced cytochrome c is oxidized by cytochrome oxidase

# ============================================================
# NEW ANNOTATIONS (missing from current set)
# ============================================================
  - term:
      id: GO:0043293
      label: apoptosome
    evidence_type: IPI
    original_reference_id: PMID:10206961
    review:
      summary: >-
        Cytochrome c is a structural component of the apoptosome, a multisubunit complex
        composed
        of Apaf-1, cytochrome c, and procaspase-9. Zou et al. 1999 (PMID:10206961)
        demonstrated
        that cytochrome c binds Apaf-1 to form a multimeric complex that recruits
        and
        activates
        procaspase-9. This CC annotation is present in the UniProt GO section (IPI:ComplexPortal)
        but was not in the GOA TSV used to generate this review. It should be added
        as it captures
        a core component annotation for the apoptotic function.
      action: NEW
      reason: >-
        Cytochrome c is a bona fide component of the apoptosome. The apoptosome annotation
        (GO:0043293) is listed in UniProt for this protein and accurately captures
        its
        structural
        role in apoptotic signaling. This is an important CC annotation complementing
        the BP
        annotation GO:0097193.
      supported_by:
        - reference_id: PMID:10206961
          supporting_text: >-
            APAF-1 oligomerization, forming a large multimeric APAF-1.cytochrome c
            complex.
            Such
            a complex can be isolated using gel filtration chromatography and is by
            itself
            sufficient
            to recruit and activate procaspase-9. The stoichiometric ratio of procaspase-9
            to
            APAF-1 is approximately 1 to 1 in the complex
references:
  - id: GO_REF:0000002
    title: Gene Ontology annotation through association of InterPro records with GO
      terms
    findings: []
  - id: GO_REF:0000033
    title: Annotation inferences using phylogenetic trees
    findings: []
  - id: GO_REF:0000043
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
    findings: []
  - id: GO_REF:0000044
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
      vocabulary mapping, accompanied by conservative changes to GO terms applied
      by UniProt
    findings: []
  - id: GO_REF:0000052
    title: Gene Ontology annotation based on curation of immunofluorescence data
    findings: []
  - id: GO_REF:0000054
    title: Gene Ontology annotation based on curation of intracellular localizations
      of expressed fusion proteins in living cells
    findings: []
  - id: PMID:8689682
    title: 'Induction of apoptotic program in cell-free extracts: requirement for
      dATP and cytochrome c.'
    findings:
      - statement: >-
          Landmark paper identifying cytochrome c as a required factor for the apoptotic
          program.
          Cell-free system showed that cytochrome c is released from mitochondria
          during
          apoptosis
          and its addition to cytosol activates the apoptotic cascade.
        supporting_text: >-
          A cell-free system based on cytosols of normally growing cells is established
          that reproduces aspects of the apoptotic program in vitro
  - id: PMID:9267021
    title: Apaf-1, a human protein homologous to C. elegans CED-4, participates in
      cytochrome c-dependent activation of caspase-3.
    findings:
      - statement: >-
          Identification and cloning of Apaf-1 as the cytochrome c-binding protein
          that
          mediates
          caspase activation. Cytochrome c binds to Apaf-1 to trigger caspase-3 activation.
        supporting_text: >-
          Cytochrome c binds to Apaf-1, an event that may trigger the activation of
          caspase-3,
          leading to apoptosis
  - id: PMID:9515723
    title: Cytochrome c in the apoptotic and antioxidant cascades.
    findings:
      - statement: >-
          Review describing the dual role of cytochrome c as a pro-apoptotic factor
          (released
          from
          mitochondria to activate caspases via Apaf-1) and as an antioxidant (oxidizing
          superoxide
          back to O2 in the IMS).
        supporting_text: >-
          cytochrome c is a pro-apoptotic factor. It is released from its places on
          the
          outer
          surface of the inner mitochondrial membrane at early steps of apoptosis
          and,
          combining
          with some cytosolic proteins, activates conversion of the latent apoptosis-promoting
          protease pro-caspase-9 to its active form
  - id: PMID:10206961
    title: An APAF-1.cytochrome c multimeric complex is a functional apoptosome that
      activates procaspase-9.
    findings:
      - statement: >-
          Reconstitution of the apoptosome using purified cytochrome c, recombinant
          APAF-1,
          and
          recombinant procaspase-9. Cytochrome c and ATP/dATP hydrolysis promote APAF-1
          oligomerization to form the apoptosome, which recruits and activates procaspase-9.
        supporting_text: >-
          the binding of cytochrome c promote APAF-1 oligomerization, forming a large
          multimeric
          APAF-1.cytochrome c complex. Such a complex can be isolated using gel filtration
          chromatography and is by itself sufficient to recruit and activate procaspase-9
  - id: PMID:10383829
    title: A soluble version of the receptor-like protein tyrosine phosphatase kappa
      stimulates neurite outgrowth via a Grb2/MEK1-dependent signaling cascade.
    findings:
      - statement: >-
          This publication is about RPTPkappa stimulating neurite outgrowth and has
          no
          apparent
          connection to cytochrome c or cellular respiration. The reference appears
          to
          be
          incorrectly linked to the CYCS cellular respiration annotation.
        supporting_text: >-
          Receptor-like protein tyrosine phosphatase kappa (RPTPkappa) is expressed
          in
          the
          nervous system in a manner consistent with a role in axonal growth and guidance
  - id: PMID:12107093
    title: Microinjection of cathepsin d induces caspase-dependent apoptosis in fibroblasts.
    findings:
      - statement: >-
          Cathepsin D microinjection into cytosol induces apoptosis with cytochrome
          c
          redistribution
          and caspase activation. Cytochrome c release from mitochondria was observed
          as part of the
          apoptotic cascade. Used as ISS reference for mouse-to-human apoptotic signaling
          transfer.
        supporting_text: >-
          microinjection of cathepsin D into the cytosol of human fibroblasts caused
          apoptosis,
          which was detected as changes in distribution of cytochrome c, cell shrinkage,
          activation
          of caspases
  - id: PMID:19393246
    title: Knockdown of human COX17 affects assembly and supramolecular organization
      of cytochrome c oxidase.
    findings:
      - statement: >-
          COX17 knockdown affects cytochrome c oxidase assembly and supercomplex organization.
          Study involved cytochrome c in the context of respiratory chain supercomplex
          function
          in the mitochondrial IMS.
        supporting_text: >-
          Assembly of cytochrome c oxidase, the terminal enzyme of the mitochondrial
          respiratory chain, requires a concerted activity of a number of chaperones
          and
          factors for the insertion of subunits, accessory proteins, cofactors and
          prosthetic groups
  - id: PMID:20671748
    title: Bcl-2 family interaction with the mitochondrial morphogenesis machinery.
    findings:
      - statement: >-
          Study on Bax/Bak-dependent mitochondrial dynamics and Bcl-2 family regulation
          of
          mitochondrial morphology. Cytochrome c release is context for apoptosis
          studies.
        supporting_text: >-
          The regulation of both mitochondrial dynamics and apoptosis is key for
          maintaining the health of a cell
  - id: PMID:20833797
    title: Phosphoproteome analysis of functional mitochondria isolated from resting
      human muscle reveals extensive phosphorylation of inner membrane protein complexes
      and enzymes.
    findings: []
  - id: PMID:21630459
    title: Proteomic characterization of the human sperm nucleus.
    findings:
      - statement: >-
          Mass spectrometry identification of 403 proteins in isolated sperm nuclei.
          Cytochrome
          c
          detection likely represents contamination from the adjacent mitochondrial
          midpiece
          sheath.
        supporting_text: >-
          sperm nuclei were obtained through CTAB treatment and isolated to over 99.9%
          purity
          without any tail fragments, acrosome or mitochondria as assessed by optical
          microscopy
          and transmission electron microscopy
  - id: PMID:25416956
    title: A proteome-scale map of the human interactome network.
    findings: []
  - id: PMID:25595453
    title: Respiratory complexes III and IV can each bind two molecules of cytochrome
      c at low ionic strength.
    findings:
      - statement: >-
          Human cytochrome c interacts with respiratory complexes III and IV with
          2:1
          stoichiometry
          at low ionic strength. Extra binding sites facilitate turnover and sliding
          of
          cytochrome c
          within respiratory supercomplexes.
        supporting_text: >-
          two cytochrome c molecules per adduct - at low ionic strength. We conclude
          that
          such extra
          binding sites at the surfaces of complexes III and IV can facilitate the
          turnover
          and
          sliding of cytochrome c molecules
  - id: PMID:25910212
    title: Widespread macromolecular interaction perturbations in human genetic disorders.
    findings: []
  - id: PMID:28514442
    title: Architecture of the human interactome defines protein communities and disease
      networks.
    findings: []
  - id: PMID:32296183
    title: A reference map of the human binary protein interactome.
    findings: []
  - id: PMID:32814053
    title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins
      and Uncovers Widespread Protein Aggregation in Affected Brains.
    findings: []
  - id: PMID:33961781
    title: Dual proteome-scale networks reveal cell-specific remodeling of the human
      interactome.
    findings: []
  - id: PMID:34800366
    title: Quantitative high-confidence human mitochondrial proteome and its dynamics
      in cellular context.
    findings: []
  - id: Reactome:R-HSA-114252
    title: Cleavage of Procaspase-3 by the apoptosome
    findings: []
  - id: Reactome:R-HSA-114254
    title: CYCS binds to APAF1
    findings: []
  - id: Reactome:R-HSA-114256
    title: CYCS:APAF1 binds procaspase-9
    findings: []
  - id: Reactome:R-HSA-114259
    title: Cleavage of Procaspase-9 to caspase-9
    findings: []
  - id: Reactome:R-HSA-114261
    title: Cleavage of Procaspase-7 by the apoptosome
    findings: []
  - id: Reactome:R-HSA-114284
    title: Release of Cytochrome c from mitochondria
    findings: []
  - id: Reactome:R-HSA-1592231
    title: Expression of CYCS
    findings: []
  - id: Reactome:R-HSA-163214
    title: Electron transfer from reduced cytochrome c to molecular oxygen
    findings: []
  - id: Reactome:R-HSA-164651
    title: Electron transfer from ubiquinol to cytochrome c of complex III
    findings: []
  - id: Reactome:R-HSA-3341294
    title: Superoxide reduces cytochrome c
    findings: []
  - id: Reactome:R-HSA-5688294
    title: SIRT5 deacetylates Cytochrome C
    findings: []
  - id: Reactome:R-HSA-6804596
    title: APAF1:CYCS binds APIP
    findings: []
  - id: Reactome:R-HSA-9627056
    title: Procaspase 9 forms dimer
    findings: []
  - id: Reactome:R-HSA-9627078
    title: XIAP binds CASP9
    findings: []
  - id: Reactome:R-HSA-9627089
    title: CASP9 is phosphorylated at T412
    findings: []
  - id: Reactome:R-HSA-9866217
    title: HCCS inserts heme into cytochrome c
    findings: []
  - id: file:human/CYCS/CYCS-deep-research-falcon.md
    title: Deep research review of CYCS gene function (Falcon provider)
    findings:
      - statement: >-
          CYCS encodes human cytochrome c, a dual-role protein essential for mitochondrial
          respiration (electron carrier from Complex III to Complex IV) and intrinsic
          apoptosis
          (released from mitochondria, binds Apaf-1 to form the apoptosome, activates
          caspase-9).
          The heme c group is covalently attached. Cytochrome c-cardiolipin interactions
          modulate
          both electron transfer and apoptotic release.
core_functions:
  - molecular_function:
      id: GO:0009055
      label: electron transfer activity
    directly_involved_in:
      - id: GO:0006122
        label: mitochondrial electron transport, ubiquinol to cytochrome c
      - id: GO:0006123
        label: mitochondrial electron transport, cytochrome c to oxygen
      - id: GO:0045333
        label: cellular respiration
    locations:
      - id: GO:0005758
        label: mitochondrial intermembrane space
      - id: GO:0005743
        label: mitochondrial inner membrane
    description: >-
      Cytochrome c is a small soluble heme-containing electron carrier protein that
      shuttles
      single electrons from Complex III (cytochrome bc1) to Complex IV (cytochrome
      c
      oxidase) in
      the mitochondrial intermembrane space. The protein accepts electrons from the
      cytochrome c1
      subunit of Complex III via its covalently bound heme c group (Fe3+ -> Fe2+)
      and
      donates
      them to cytochrome c oxidase (Fe2+ -> Fe3+). This electron transfer function
      is
      essential
      for oxidative phosphorylation and cellular respiration. The heme c prosthetic
      group is
      covalently attached via thioether bonds to Cys15 and Cys18, with His18 and Met80
      as axial
      iron ligands. Cytochrome c is loosely associated with the inner mitochondrial
      membrane
      surface via electrostatic interactions and cardiolipin binding, operating within
      the IMS.
    supported_by:
      - reference_id: PMID:9515723
        supporting_text: >-
          The reduced cytochrome c is oxidized by cytochrome oxidase
      - reference_id: PMID:25595453
        supporting_text: >-
          two cytochrome c molecules per adduct - at low ionic strength. We conclude
          that
          such
          extra binding sites at the surfaces of complexes III and IV can facilitate
          the
          turnover
          and sliding of cytochrome c molecules
      - reference_id: file:human/CYCS/CYCS-deep-research-falcon.md
        supporting_text: >-
          cytochrome c shuttles electrons from complex III (cytochrome bc1) to complex
          IV
          (cytochrome c oxidase) in the inner mitochondrial membrane cristae region,
          supporting
          oxidative phosphorylation
  - molecular_function:
      id: GO:0009055
      label: electron transfer activity
    directly_involved_in:
      - id: GO:0097193
        label: intrinsic apoptotic signaling pathway
    locations:
      - id: GO:0005829
        label: cytosol
    description: >-
      Upon mitochondrial outer membrane permeabilization (MOMP) triggered by pro-apoptotic
      Bcl-2
      family members (BAX/BAK), cytochrome c is released from the mitochondrial IMS
      into the
      cytosol. In the cytosol, cytochrome c binds to Apaf-1, promoting Apaf-1 oligomerization
      and formation of the apoptosome, a heptameric wheel-like complex. The apoptosome
      recruits
      and activates procaspase-9, which in turn cleaves and activates effector caspases
      (caspase-3,
      caspase-7), executing the apoptotic program. This dual function of cytochrome
      c -- electron
      carrier in the ETC and apoptotic trigger when released -- makes it a classic
      moonlighting
      protein. The G42S variant in CYCS enhances apoptotic activation and causes thrombocytopenia
      type 4 (THC4), demonstrating the clinical significance of this function.
    supported_by:
      - reference_id: PMID:8689682
        supporting_text: >-
          protein sequence revealed that this protein is cytochrome c...Cells undergoing
          apoptosis
          in vivo showed increased release of cytochrome c to their cytosol, suggesting
          that
          mitochondria may function in apoptosis by releasing cytochrome c
      - reference_id: PMID:9267021
        supporting_text: >-
          Cytochrome c binds to Apaf-1, an event that may trigger the activation of
          caspase-3,
          leading to apoptosis
      - reference_id: PMID:10206961
        supporting_text: >-
          the binding of cytochrome c promote APAF-1 oligomerization, forming a large
          multimeric
          APAF-1.cytochrome c complex. Such a complex can be isolated using gel filtration
          chromatography and is by itself sufficient to recruit and activate procaspase-9
    in_complex:
      id: GO:0043293
      label: apoptosome