BNIP3L (NIX) is a tail-anchored, atypical BH3-containing member of the BNIP3/NIP3 family that is inserted into the mitochondrial outer membrane via its C-terminal transmembrane helix, with its N-terminal disordered region facing the cytosol. Its principal, conserved function is as a selective autophagy (mitophagy) receptor: an LC3-interacting region in the cytosolic domain binds Atg8-family proteins (LC3 and GABARAP/GABARAPL1/GABARAPL2), tethering mitochondria to the forming autophagosome and driving their programmed autophagic clearance. This is most prominent during terminal erythroid/reticulocyte maturation and other developmentally programmed or stress-induced episodes of mitochondrial turnover. NIX also participates in non-canonical mitochondrial quality control through ROS-dependent interaction with SPATA18/MIEAP, and under hypoxia it is induced by HIF and promotes pro-survival macroautophagy via its atypical BH3 domain. Although first described as a pro-apoptotic BCL-2-family protein, its effects on cell death are context-dependent and direction-dependent (it can both promote and inhibit cell death) and act largely through mitochondrial membrane permeability/necrosis rather than classical cytochrome-c/caspase apoptosis. Beyond mitochondria, NIX can independently localize to peroxisomes and act as a selective autophagy receptor for their clearance (pexophagy), broadening its cargo selectivity. NIX abundance is held in check by constitutive ubiquitin-mediated turnover: an SCF(FBXL4) ubiquitin ligase complex at the mitochondrial outer membrane, with the phosphatase PPTC7 as a cofactor, degrades NIX (and BNIP3) to restrain basal mitophagy, while hypoxia/HIF signaling induces NIX transcription. NIX is also exploited by several viruses, which hijack NIX-mediated mitophagy to degrade mitochondrial antiviral signaling components.
Definition: A protein-tethering activity in which a mitochondrial outer membrane protein bridges the mitochondrion to an Atg8-family protein (LC3/GABARAP) via an LC3-interacting region (LIR), thereby targeting the mitochondrion for selective autophagic degradation (mitophagy).
Justification: NIX/BNIP3L's defining molecular activity is acting as a selective autophagy (mitophagy) receptor that bridges the mitochondrial outer membrane to Atg8-family proteins (LC3/GABARAP) via its LIR motif. No existing molecular-function term in the seeded annotation set captures this cargo-receptor activity; the closest existing term used is protein homodimerization activity, which is incomplete.
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0043065 positive regulation of apoptotic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: NIX/BNIP3L was first characterized as a pro-apoptotic BCL-2/NIP3-family protein and can promote cell death in some contexts, but this is direction-dependent and atypical (necrosis/membrane permeability rather than classical caspase apoptosis). Reason: The pro-apoptotic role is genuine but secondary and context-dependent relative to the conserved mitophagy-receptor function; the same gene also has negative-regulation-of-apoptosis annotations, underscoring that cell-death regulation is contextual. Supporting Evidence: PMID:9973195 Overexpression of BNIP3alpha in transfected cells results in apoptosis and suppresses the antiapoptosis activity of E1B-19K and BCL-xL. PMID:21264228 in contrast to other mitochondrial Bcl-2 family proteins, NIX and BNIP3 are not involved in the release of cytochrome c and the resulting caspase-dependent apoptosis, but rather related to necrosis through the regulation of mitochondrial permeability transition pore (MPTP) |
| GO:0043653 mitochondrial fragmentation involved in apoptotic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Mitochondrial fragmentation in an apoptotic context is a secondary, contextual aspect of NIX biology rather than its core mitophagy-receptor function. Reason: NIX can promote mitochondrial membrane permeabilization/necrosis-related death, but the conserved core function is selective autophagic clearance of mitochondria, not apoptotic fragmentation. Supporting Evidence: PMID:21264228 in contrast to other mitochondrial Bcl-2 family proteins, NIX and BNIP3 are not involved in the release of cytochrome c and the resulting caspase-dependent apoptosis, but rather related to necrosis through the regulation of mitochondrial permeability transition pore (MPTP) |
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: ER localization is reported for NIX (it was detected in nuclear envelope, ER and mitochondria, and linked to ER Ca2+ handling), but it is a secondary site relative to the mitochondrial outer membrane where the mitophagy-receptor function operates. Reason: ER localization is documented but is not the primary functional compartment; the is_active_in qualifier overstates ER as a site of NIX activity. Supporting Evidence: PMID:10381623 localizes in nuclear envelope, endoplasmic reticulum and mitochondria PMID:21264228 NIX was also shown to localize to endoplasmic reticulum (ER) and increase the store of Ca++, leading to Ca++ influx into mitochondria and cell death |
| GO:0005741 mitochondrial outer membrane | IBA GO_REF:0000033 | ACCEPT | Summary: The mitochondrial outer membrane is the core functional location of NIX, where its C-terminal transmembrane anchor inserts and its cytosolic LIR engages the autophagy machinery. Reason: This is the principal functional compartment for the mitophagy-receptor activity and is strongly supported by multiple independent studies. Supporting Evidence: PMID:20200478 Nix is a mitochondrial outer membrane protein that is required for mitochondrial clearance during erythrocyte maturation. PMID:21264228 A mitochondrial outer membrane protein NIX interacted with Mieap in a ROS-dependent manner via the BH3 domain of NIX and the coiled-coil domain of Mieap. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: A nuclear/nuclear-envelope localization derives from the original B5 study; it is weakly supported and is not the functional compartment for the mitophagy-receptor role. Reason: is_active_in nucleus is not supported by a defined nuclear function; the only relevant primary data describe nuclear envelope localization, likely reflecting tail-anchored membrane behavior, not nucleoplasmic activity. Supporting Evidence: PMID:10381623 localizes in nuclear envelope, endoplasmic reticulum and mitochondria |
| GO:0005635 nuclear envelope | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Nuclear envelope localization is reported in the original B5 study (with associated lamin binding), but it is a secondary, weakly characterized site rather than the functional mitophagy compartment. Reason: Nuclear envelope localization is documented experimentally but is not where the conserved mitophagy-receptor function acts; retained as non-core. Supporting Evidence: PMID:10381623 localizes in nuclear envelope, endoplasmic reticulum and mitochondria |
| GO:0005635 nuclear envelope | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Automated subcellular-location transfer of nuclear envelope localization, consistent with the experimental B5 data. Reason: Consistent with documented nuclear envelope localization but secondary to the mitochondrial outer membrane function. Supporting Evidence: PMID:10381623 localizes in nuclear envelope, endoplasmic reticulum and mitochondria |
| GO:0005740 mitochondrial envelope | IEA GO_REF:0000002 | MODIFY | Summary: Mitochondrial envelope is a less specific parent of the mitochondrial outer membrane, where NIX is actually anchored. Reason: The more precise and well-supported localization is the mitochondrial outer membrane; replace the broader envelope term. Proposed replacements: mitochondrial outer membrane Supporting Evidence: PMID:20200478 Nix is a mitochondrial outer membrane protein that is required for mitochondrial clearance during erythrocyte maturation. |
| GO:0005741 mitochondrial outer membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Automated location transfer of the well-supported mitochondrial outer membrane localization. Reason: Strongly supported as the core functional compartment. Supporting Evidence: PMID:20200478 Nix is a mitochondrial outer membrane protein that is required for mitochondrial clearance during erythrocyte maturation. |
| GO:0005783 endoplasmic reticulum | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Automated transfer of ER localization, consistent with experimental detection of NIX in the ER. Reason: ER localization is documented but is a secondary site relative to the mitochondrial outer membrane. Supporting Evidence: PMID:10381623 localizes in nuclear envelope, endoplasmic reticulum and mitochondria |
| GO:0016020 membrane | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: NIX is a single-pass tail-anchored membrane protein, so generic membrane localization is correct but uninformative. Reason: The generic membrane term is subsumed by the specific and well-supported mitochondrial outer membrane localization. Supporting Evidence: file:human/BNIP3L/BNIP3L-uniprot.txt Single-pass |
| GO:0043065 positive regulation of apoptotic process | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Automated transfer of the pro-apoptotic process annotation; genuine but context-dependent and not the core function. Reason: Cell-death promotion by NIX is contextual and direction-dependent; secondary to mitophagy. Supporting Evidence: PMID:9973195 Overexpression of BNIP3alpha in transfected cells results in apoptosis and suppresses the antiapoptosis activity of E1B-19K and BCL-xL. |
| GO:0005515 protein binding | IPI PMID:10381623 A novel adenovirus E1B19K-binding protein B5 inhibits apopto... | MARK AS OVER ANNOTATED | Summary: Generic protein-binding annotation; the underlying B5 data describe specific self-association and BNIP3 heterodimerization, captured better by homodimerization activity. Reason: Bare protein binding is uninformative; the specific interactions are represented by the identical protein binding / homodimerization annotations from this same study. Supporting Evidence: PMID:10381623 B5 binds strongly to Nip3 and itself |
| GO:0005515 protein binding | IPI PMID:16189514 Towards a proteome-scale map of the human protein-protein in... | MARK AS OVER ANNOTATED | Summary: High-throughput interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from a proteome-scale interaction map does not identify an interpretable NIX function. |
| GO:0005515 protein binding | IPI PMID:19060904 An empirical framework for binary interactome mapping. | MARK AS OVER ANNOTATED | Summary: High-throughput interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from a binary interactome dataset does not specify a meaningful function. |
| GO:0005515 protein binding | IPI PMID:21516116 Next-generation sequencing to generate interactome datasets. | MARK AS OVER ANNOTATED | Summary: High-throughput interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from an interactome-mapping method is not functionally specific. |
| GO:0005515 protein binding | IPI PMID:22645275 Identification of novel ATP13A2 interactors and their role i... | MARK AS OVER ANNOTATED | Summary: Generic protein-binding annotation from an ATP13A2/alpha-synuclein interactome study; uninformative for core NIX function. Reason: Bare protein binding does not specify a NIX function; the interaction is not tied to core mitophagy biology. |
| GO:0005515 protein binding | IPI PMID:24316735 Orphan nuclear receptor TR3 acts in autophagic cell death vi... | MARK AS OVER ANNOTATED | Summary: Generic protein-binding annotation from a TR3/NR4A1 autophagic-cell-death study; uninformative as bare protein binding. Reason: The term protein binding is too general; the NR4A1 interaction is not informative as core NIX function. |
| GO:0005515 protein binding | IPI PMID:24981860 Human-chromatin-related protein interactions identify a deme... | MARK AS OVER ANNOTATED | Summary: High-throughput chromatin-related interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from a large-scale interaction study does not specify a NIX function. |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: High-throughput interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from a proteome-scale interactome map is not functionally specific. |
| GO:0005515 protein binding | IPI PMID:25910212 Widespread macromolecular interaction perturbations in human... | MARK AS OVER ANNOTATED | Summary: High-throughput interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from a disease-interactome perturbation study is not functionally specific. |
| GO:0005515 protein binding | IPI PMID:27107012 Pooled-matrix protein interaction screens using Barcode Fusi... | MARK AS OVER ANNOTATED | Summary: High-throughput interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from a pooled interaction screen does not specify a NIX function. |
| GO:0005515 protein binding | IPI PMID:28514442 Architecture of the human interactome defines protein commun... | MARK AS OVER ANNOTATED | Summary: High-throughput interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from a large-scale interactome study is not functionally specific. |
| GO:0005515 protein binding | IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari... | MARK AS OVER ANNOTATED | Summary: High-throughput interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from a variant-interaction study is not functionally specific. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: High-throughput interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from a reference binary interactome map is not functionally specific. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: High-throughput interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from a cell-specific interactome remodeling study is not functionally specific. |
| GO:0005515 protein binding | IPI PMID:34845370 SARS-CoV-2 ORF10 suppresses the antiviral innate immune resp... | MARK AS OVER ANNOTATED | Summary: This protein-binding annotation reflects the specific, functionally important interaction of NIX with SARS-CoV-2 ORF10 and LC3B during virus-hijacked mitophagy; as bare protein binding it is uninformative. Reason: The underlying interaction is meaningful (ORF10/LC3B binding driving NIX-mediated mitophagy), but the generic protein binding term does not capture it; the antiviral mitophagy biology is curated under defense response to virus. Supporting Evidence: PMID:34845370 ORF10 was translocated to mitochondria by interacting with the mitophagy receptor Nip3-like protein X (NIX) and induced mitophagy through its interaction with both NIX and LC3B |
| GO:0005515 protein binding | IPI PMID:39526800 A comprehensive two-hybrid analysis to explore the Legionell... | MARK AS OVER ANNOTATED | Summary: High-throughput Legionella effector two-hybrid interactome protein-binding annotation; uninformative for NIX function. Reason: Generic protein binding from a pathogen-effector interactome screen is not functionally specific for NIX. |
| GO:0005515 protein binding | IPI PMID:9973195 BNIP3alpha: a human homolog of mitochondrial proapoptotic pr... | MARK AS OVER ANNOTATED | Summary: Generic protein-binding annotation; the underlying data describe specific interactions with E1B-19K, BCL-2 and BCL-xL, not informative as bare binding. Reason: Bare protein binding is uninformative; the specific anti-apoptotic-protein interactions are better represented elsewhere. Supporting Evidence: PMID:9973195 BNIP3alpha interacts with viral antiapoptosis protein E1B-19K and cellular antiapoptosis proteins BCL-2 and BCL-xL. |
| GO:0042802 identical protein binding | IPI PMID:10381623 A novel adenovirus E1B19K-binding protein B5 inhibits apopto... | ACCEPT | Summary: NIX/B5 self-associates, and the original study directly shows it binds itself; identical protein binding (self-association) is supported. Reason: Self-association is directly demonstrated and is a genuine, informative molecular property of NIX. Supporting Evidence: PMID:10381623 B5 binds strongly to Nip3 and itself |
| GO:0042802 identical protein binding | IPI PMID:16189514 Towards a proteome-scale map of the human protein-protein in... | ACCEPT | Summary: NIX self-association is recorded as identical protein binding in a high-throughput interactome (IntAct O60238-O60238); consistent with directly demonstrated self-association. Reason: NIX self-association is independently supported by direct biochemistry; the high-throughput identical-protein-binding hit is consistent and informative. Supporting Evidence: PMID:10381623 B5 binds strongly to Nip3 and itself |
| GO:0042802 identical protein binding | IPI PMID:21516116 Next-generation sequencing to generate interactome datasets. | ACCEPT | Summary: NIX self-association recorded as identical protein binding from interactome mapping; consistent with demonstrated self-association. Reason: Consistent with directly demonstrated NIX self-association and informative as a homodimerization property. Supporting Evidence: PMID:10381623 B5 binds strongly to Nip3 and itself |
| GO:0042802 identical protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | ACCEPT | Summary: NIX self-association recorded as identical protein binding from a proteome-scale interactome; consistent with demonstrated self-association. Reason: Consistent with directly demonstrated NIX self-association. Supporting Evidence: PMID:10381623 B5 binds strongly to Nip3 and itself |
| GO:0042802 identical protein binding | IPI PMID:27107012 Pooled-matrix protein interaction screens using Barcode Fusi... | ACCEPT | Summary: NIX self-association recorded as identical protein binding from a pooled interaction screen; consistent with demonstrated self-association. Reason: Consistent with directly demonstrated NIX self-association. Supporting Evidence: PMID:10381623 B5 binds strongly to Nip3 and itself |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: General mitochondrial localization; correct but less specific than the mitochondrial outer membrane localization. Reason: Accurate but subsumed by the more precise mitochondrial outer membrane annotation. Supporting Evidence: PMID:9973195 Like BNIP3, BNIP3alpha seems to be predominantly localized in mitochondria. |
| GO:0010917 negative regulation of mitochondrial membrane potential | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: NIX/BNIP3 can affect mitochondrial membrane potential/permeability (linked to necrosis and to depolarization-triggered mitophagy), a contextual mitochondrial effect. Reason: Effects on membrane potential are documented but are a downstream/contextual aspect rather than the core mitophagy-receptor activity. Supporting Evidence: PMID:21264228 related to necrosis through the regulation of mitochondrial permeability transition pore (MPTP) |
| GO:0035794 positive regulation of mitochondrial membrane permeability | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: NIX/BNIP3 are linked to opening of the mitochondrial permeability transition pore and necrosis-related membrane permeabilization, a contextual function. Reason: Supported as a contextual mitochondrial membrane effect; secondary to mitophagy-receptor activity. Supporting Evidence: PMID:21264228 related to necrosis through the regulation of mitochondrial permeability transition pore (MPTP) |
| GO:0042802 identical protein binding | IEA GO_REF:0000120 | ACCEPT | Summary: Automated identical-protein-binding annotation, consistent with directly demonstrated NIX self-association. Reason: Consistent with documented NIX self-association. Supporting Evidence: PMID:10381623 B5 binds strongly to Nip3 and itself |
| GO:1901524 regulation of mitophagy | IEA GO_REF:0000107 | ACCEPT | Summary: Regulation of mitophagy is a core process for NIX, which acts as a mitochondrial receptor connecting mitochondria to the autophagy machinery via LC3/GABARAP. Reason: Mitophagy is the defining conserved function of NIX and is strongly supported. Supporting Evidence: PMID:20200478 Nix is a mitochondrial receptor that can directly connect to one of the autophagic machinery components, the Atg8 homologs LC3 and GABARAP. |
| GO:1903747 regulation of protein localization to mitochondrion | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: NIX recruits autophagy machinery (LC3/GABARAP) to mitochondria; this can be viewed as regulating protein localization to the mitochondrion, but it is better represented by mitophagy receptor activity. Reason: The annotation captures a mechanistic aspect (recruitment of Atg8-family proteins to mitochondria) of the core mitophagy function but as a broad regulatory term is less precise; retained as non-core. Supporting Evidence: PMID:20200478 Nix is a mitochondrial receptor that can directly connect to one of the autophagic machinery components, the Atg8 homologs LC3 and GABARAP. |
| GO:0005739 mitochondrion | IDA GO_REF:0000052 | KEEP AS NON CORE | Summary: Immunofluorescence-based mitochondrial localization, consistent with the predominant mitochondrial localization of NIX. Reason: Accurate but subsumed by the more precise mitochondrial outer membrane localization. Supporting Evidence: PMID:9973195 Like BNIP3, BNIP3alpha seems to be predominantly localized in mitochondria. |
| GO:0016607 nuclear speck | IDA GO_REF:0000052 | MARK AS OVER ANNOTATED | Summary: A nuclear speck localization (HPA immunofluorescence) is weakly supported and inconsistent with the established tail-anchored mitochondrial outer membrane biology of NIX. Reason: No defined nuclear-speck function exists for NIX; this single-source localization likely reflects antibody/overexpression artifact and is not the functional compartment. |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | KEEP AS NON CORE | Summary: High-throughput mitochondrial proteome localization, consistent with NIX being a mitochondrial protein. Reason: Accurate but subsumed by the more precise mitochondrial outer membrane localization. Supporting Evidence: PMID:34800366 mitochondrial proteome |
| GO:0043069 negative regulation of programmed cell death | IGI PMID:19273585 Hypoxia-induced autophagy is mediated through hypoxia-induci... | KEEP AS NON CORE | Summary: Under hypoxia, HIF-induced BNIP3/BNIP3L promote pro-survival autophagy and their ablation triggers cell death, supporting a negative regulation of programmed cell death role in this context. Reason: Supported by genetic evidence but contextual (hypoxia/survival); secondary to the core mitophagy-receptor function. Supporting Evidence: PMID:19273585 the ablation of BNIP3 and/or BNIP3L triggers cell death PMID:19273585 Hypoxia-induced autophagy via BNIP3 and BNIP3L is clearly a survival mechanism that promotes tumor progression. |
| GO:0016239 positive regulation of macroautophagy | IGI PMID:19273585 Hypoxia-induced autophagy is mediated through hypoxia-induci... | ACCEPT | Summary: BNIP3/BNIP3L are required for hypoxia-induced macroautophagy and their atypical BH3 domains can initiate autophagy by disrupting the Bcl-2-Beclin1 complex. Reason: Positive regulation of macroautophagy is well supported by combined silencing/ectopic expression and BH3-peptide experiments, and is closely tied to the autophagy-receptor biology of NIX. Supporting Evidence: PMID:19273585 the combined silencing of these two HIF targets suppresses hypoxia-mediated autophagy PMID:19273585 the ectopic expression of both BNIP3 and BNIP3L in normoxia activates autophagy |
| GO:0071456 cellular response to hypoxia | IGI PMID:19273585 Hypoxia-induced autophagy is mediated through hypoxia-induci... | KEEP AS NON CORE | Summary: BNIP3L is a HIF target that mediates hypoxia-induced autophagy, supporting a role in the cellular response to hypoxia. Reason: Supported as part of the hypoxia/HIF-autophagy axis but is a contextual upstream process rather than the core molecular function. Supporting Evidence: PMID:19273585 the combined silencing of these two HIF targets suppresses hypoxia-mediated autophagy |
| GO:0005741 mitochondrial outer membrane | TAS Reactome:R-HSA-6798004 | ACCEPT | Summary: Reactome-curated mitochondrial outer membrane localization (TP53 stimulates BNIP3L expression pathway). Reason: Consistent with the well-supported core localization. Supporting Evidence: PMID:20200478 Nix is a mitochondrial outer membrane protein that is required for mitochondrial clearance during erythrocyte maturation. |
| GO:0005741 mitochondrial outer membrane | TAS Reactome:R-HSA-6801195 | ACCEPT | Summary: Reactome-curated mitochondrial outer membrane localization (STEAP3 binds BNIP3L pathway). Reason: Consistent with the well-supported core localization. Supporting Evidence: PMID:20200478 Nix is a mitochondrial outer membrane protein that is required for mitochondrial clearance during erythrocyte maturation. |
| GO:0005515 protein binding | IPI PMID:20200478 Nix, a receptor protein for mitophagy in mammals. | MARK AS OVER ANNOTATED | Summary: This protein-binding annotation reflects the functionally central interaction of NIX with the Atg8 homologs LC3/GABARAP, but as bare protein binding it is uninformative. Reason: The underlying LC3/GABARAP interaction is the molecular basis of NIX mitophagy-receptor activity; bare protein binding does not capture this and the function is curated under regulation of mitophagy. Supporting Evidence: PMID:20200478 Nix is a mitochondrial receptor that can directly connect to one of the autophagic machinery components, the Atg8 homologs LC3 and GABARAP. |
| GO:0043065 positive regulation of apoptotic process | IDA PMID:9973195 BNIP3alpha: a human homolog of mitochondrial proapoptotic pr... | KEEP AS NON CORE | Summary: Overexpression of BNIP3alpha induced apoptosis in transfected cells, providing direct (if overexpression-based) evidence for a pro-apoptotic role. Reason: Direct evidence supports a pro-apoptotic capacity, but it is context-dependent/overexpression-driven and secondary to the conserved mitophagy function. Supporting Evidence: PMID:9973195 Overexpression of BNIP3alpha in transfected cells results in apoptosis and suppresses the antiapoptosis activity of E1B-19K and BCL-xL. |
| GO:0005515 protein binding | IPI PMID:21264221 Possible existence of lysosome-like organella within mitocho... | MARK AS OVER ANNOTATED | Summary: Generic protein-binding annotation associated with the Mieap/MALM mitochondrial quality-control studies; uninformative as bare binding. Reason: Bare protein binding is uninformative; the relevant NIX-SPATA18/Mieap interaction is curated via the mitochondrial protein catabolic process annotation. |
| GO:0005741 mitochondrial outer membrane | IMP PMID:21264228 Mieap, a p53-inducible protein, controls mitochondrial quali... | ACCEPT | Summary: NIX localizes to and acts at the mitochondrial outer membrane, where it interacts with Mieap via its BH3 domain; mutational/localization analysis supports this compartment. Reason: Directly supported core localization. Supporting Evidence: PMID:21264228 A mitochondrial outer membrane protein NIX interacted with Mieap in a ROS-dependent manner via the BH3 domain of NIX and the coiled-coil domain of Mieap. |
| GO:0035694 mitochondrial protein catabolic process | IMP PMID:21264228 Mieap, a p53-inducible protein, controls mitochondrial quali... | ACCEPT | Summary: NIX is an essential mediator of MALM (Mieap-induced accumulation of lysosome-like organelles within mitochondria), a non-canonical process that degrades oxidized mitochondrial proteins; NIX deficiency impairs MALM. Reason: Loss-of-function (NIX knockdown) directly impairs MALM, supporting NIX involvement in mitochondrial protein catabolism within the mitochondrial quality-control context. Supporting Evidence: PMID:21264228 Deficiency of NIX also completely impaired MALM. |
| GO:0005521 lamin binding | IPI PMID:10381623 A novel adenovirus E1B19K-binding protein B5 inhibits apopto... | KEEP AS NON CORE | Summary: Lamin binding derives from the original B5/nuclear-envelope study; it is a specific but secondary interaction not central to the mitophagy-receptor function. Reason: Retained as a specific (non-generic) binding annotation, but it is contextual to the nuclear-envelope localization and not the core function. Supporting Evidence: PMID:10381623 localizes in nuclear envelope, endoplasmic reticulum and mitochondria |
| GO:0005521 lamin binding | IDA PMID:10381623 A novel adenovirus E1B19K-binding protein B5 inhibits apopto... | KEEP AS NON CORE | Summary: Direct-assay lamin binding from the original B5 study; specific but secondary. Reason: Specific binding annotation tied to nuclear-envelope localization; not the core function. Supporting Evidence: PMID:10381623 localizes in nuclear envelope, endoplasmic reticulum and mitochondria |
| GO:0005635 nuclear envelope | IDA PMID:10381623 A novel adenovirus E1B19K-binding protein B5 inhibits apopto... | KEEP AS NON CORE | Summary: Direct localization of B5/NIX to the nuclear envelope in the original study; secondary site. Reason: Documented but secondary localization relative to the mitochondrial outer membrane. Supporting Evidence: PMID:10381623 localizes in nuclear envelope, endoplasmic reticulum and mitochondria |
| GO:0005739 mitochondrion | IDA PMID:10381623 A novel adenovirus E1B19K-binding protein B5 inhibits apopto... | KEEP AS NON CORE | Summary: Direct mitochondrial localization in the original B5 study. Reason: Accurate but subsumed by the more precise mitochondrial outer membrane localization. Supporting Evidence: PMID:10381623 localizes in nuclear envelope, endoplasmic reticulum and mitochondria |
| GO:0005783 endoplasmic reticulum | IDA PMID:10381623 A novel adenovirus E1B19K-binding protein B5 inhibits apopto... | KEEP AS NON CORE | Summary: Direct ER localization in the original B5 study; secondary site. Reason: Documented but secondary localization relative to the mitochondrial outer membrane. Supporting Evidence: PMID:10381623 localizes in nuclear envelope, endoplasmic reticulum and mitochondria |
| GO:0016020 membrane | TAS PMID:10381623 A novel adenovirus E1B19K-binding protein B5 inhibits apopto... | MARK AS OVER ANNOTATED | Summary: NIX/B5 contains a C-terminal transmembrane region; generic membrane localization is correct but uninformative. Reason: Subsumed by the specific mitochondrial outer membrane localization. Supporting Evidence: PMID:10381623 contains the putative BH3 and transmembrane regions |
| GO:0042803 protein homodimerization activity | IDA PMID:10381623 A novel adenovirus E1B19K-binding protein B5 inhibits apopto... | ACCEPT | Summary: NIX/B5 self-associates (binds itself), supporting protein homodimerization activity as a genuine molecular property. Reason: Directly demonstrated self-association; informative homodimerization activity. Supporting Evidence: PMID:10381623 B5 binds strongly to Nip3 and itself |
| GO:0043066 negative regulation of apoptotic process | IDA PMID:10381623 A novel adenovirus E1B19K-binding protein B5 inhibits apopto... | KEEP AS NON CORE | Summary: In the original B5 study, NIX did not itself induce apoptosis but inhibited Nip3(BNIP3)-induced apoptosis, supporting an anti-apoptotic capacity in this context. Reason: This anti-apoptotic effect is genuine but direction- and context-dependent (the same protein can also promote death); secondary to mitophagy. Supporting Evidence: PMID:10381623 B5 does not induce apoptosis, but inhibits apoptosis induced by Nip3 |
| GO:0005739 mitochondrion | IDA PMID:9973195 BNIP3alpha: a human homolog of mitochondrial proapoptotic pr... | KEEP AS NON CORE | Summary: Direct mitochondrial localization of BNIP3alpha/NIX. Reason: Accurate but subsumed by the more precise mitochondrial outer membrane localization. Supporting Evidence: PMID:9973195 Like BNIP3, BNIP3alpha seems to be predominantly localized in mitochondria. |
| GO:0051607 defense response to virus | IDA PMID:9973195 BNIP3alpha: a human homolog of mitochondrial proapoptotic pr... | REMOVE | Summary: The cited 1999 BNIP3alpha paper is about apoptosis/anti-apoptotic-protein interactions and does not provide direct evidence for defense response to virus; the genuine antiviral connection (NIX-mediated mitophagy degrading MAVS) is established by later work, but viruses hijack this for immune evasion rather than NIX acting in host antiviral defense. Reason: The original reference (PMID:9973195) was reviewed and is about apoptosis/anti-apoptotic-protein interactions; it provides no evidence for a defense-response-to-virus role (this is therefore a removal on reviewed evidence, not an UNDECIDED due to inaccessible literature). Later literature (PMID:34845370) shows NIX-mediated mitophagy is hijacked by SARS-CoV-2 ORF10 to degrade MAVS and suppress innate immunity, the opposite of host antiviral defense; KSHV vIRF-1 similarly co-opts NIX. The annotation is unlikely to be correct based on the combined evidence. Supporting Evidence: PMID:34845370 ORF10 was translocated to mitochondria by interacting with the mitophagy receptor Nip3-like protein X (NIX) and induced mitophagy through its interaction with both NIX and LC3B PMID:34845370 NIX-mediated mitophagy is responsible for the elimination of spontaneously aggregated MAVS |
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Download this section (compressed HTML)Q: Does human NIX have a genuine host-protective antiviral function, or is NIX-mediated mitophagy primarily a target that diverse viruses hijack (e.g., SARS-CoV-2 ORF10, KSHV vIRF-1) to degrade MAVS and evade innate immunity?
Suggested experts: He H, Choi YB
Q: How is the balance between NIX-driven pro-survival mitophagy and NIX-associated cell death (necrosis/membrane permeabilization) controlled in a given cell type and stress context?
Suggested experts: Mazure NM, Dorn GW
Q: To what extent is NIX-mediated pexophagy a distinct cargo-selection program versus a by-product of shared upstream (iron-chelation/HIF) signaling, and is the peroxisomal pool of NIX targeted or regulated differently from the mitochondrial pool?
Suggested experts: Ganley IG, Boya P
Q: Is the FBXL4/PPTC7-mediated constitutive turnover of NIX a general rheostat for basal mitophagy across tissues, and does failure of this turnover (e.g., FBXL4 variants) cause disease specifically through NIX rather than BNIP3 accumulation?
Suggested experts: Pagan JK, Niemi NM
Experiment: Compare wild-type NIX with LIR-motif point mutants (abolishing LC3/GABARAP binding) for their ability to rescue mitochondrial clearance during reticulocyte maturation and stress-induced mitophagy in NIX-null cells, using flow cytometry of mitochondrial mass and mito-Keima/mito-QC reporters.
Hypothesis: NIX functions as an LIR-dependent mitophagy receptor whose Atg8-family binding is required for programmed mitochondrial clearance.
Type: structure-function rescue and mitophagy flux assay
Experiment: Knock out NIX in cells and measure MAVS levels, type I interferon induction, and viral replication with and without virus-encoded mitophagy inducers (e.g., ORF10), distinguishing host-protective versus virus-exploited roles.
Hypothesis: NIX-mediated mitophagy is required for MAVS turnover and shapes innate antiviral signaling.
Type: loss-of-function antiviral signaling assay
Experiment: In NIX-null cells reconstituted with wild-type versus LIR-mutant NIX, quantify pexophagy flux (pexo-QC/pexophagy reporters and peroxisomal marker PMP70 loss) under iron chelation and during cardiomyocyte/erythroid differentiation, and use organelle fractionation plus targeted (peroxisome- vs mitochondria-restricted) NIX constructs to test whether peroxisomal cargo selection is separable from mitochondrial mitophagy.
Hypothesis: NIX acts as a selective autophagy receptor for peroxisomes (pexophagy) in addition to mitochondria, using a peroxisome-localized pool distinct from its mitochondrial pool.
Type: structure-function rescue and selective-autophagy flux assay
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