Pik3c2a encodes phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha (PI3K-C2alpha), a class II phosphoinositide 3-kinase of about 190 kDa with an N-terminal clathrin-binding region, a Ras-binding domain, a C2 domain, a helical domain, the PI3K catalytic domain, and C-terminal PX and C2 domains. It phosphorylates phosphatidylinositol to phosphatidylinositol 3-phosphate (PI3P) and phosphatidylinositol 4-phosphate to phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2), is relatively insensitive to wortmannin, and is activated by clathrin binding. It associates with clathrin-coated pits at the plasma membrane, clathrin-coated vesicles (co-purifying with rat brain CCVs) and the trans-Golgi network, with additional pools at recycling endosomes near the cilium base and in the nucleus. PI(3,4)P2 made by PI3K-C2alpha drives maturation of late-stage clathrin-coated pits, and its PI3P pools support endosomal trafficking, Rab11 activation and ciliogenesis, and autophagosome biogenesis. In rat neuroendocrine PC12 cells and INS1 insulinoma cells it is required for regulated exocytosis of secretory granules (ATP-dependent priming and insulin granule fusion). In mammals it is essential for embryonic angiogenesis, vascular barrier function and kidney podocyte maintenance, and loss-of-function causes a human syndromic disorder with ciliary dysfunction.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular-location mapping to nucleus (ARBA-based for this TrEMBL entry); supported by human ortholog data. Reason: Human PI3K-C2alpha has a nuclear pool enriched in nuclear speckles, mapped to a C2-domain nuclear localisation signal (KRKTKISRKTR) that is conserved in the rat sequence. The nuclear pool has no established catalytic role, so the location is real but peripheral to the membrane-trafficking function. Supporting Evidence: PMID:11606566 Homo sapiens phosphoinositide 3-kinase C2alpha (HsPI3K-C2alpha) has dual cellular localization present in the cytoplasm and in the nucleus PMID:11606566 in the nucleus HsPI3K-C2alpha is enriched at distinct subnuclear domains known as nuclear speckles |
| GO:0005634 nucleus | ISO GO_REF:0000121 | KEEP AS NON CORE | Summary: ISO from human O00443 (EXP, PMID:11606566): nuclear pool of PI3K-C2alpha. Reason: Human PI3K-C2alpha has a nuclear pool enriched in nuclear speckles, mapped to a C2-domain nuclear localisation signal (KRKTKISRKTR) that is conserved in the rat sequence. The nuclear pool has no established catalytic role, so the location is real but peripheral to the membrane-trafficking function. Supporting Evidence: PMID:11606566 Homo sapiens phosphoinositide 3-kinase C2alpha (HsPI3K-C2alpha) has dual cellular localization present in the cytoplasm and in the nucleus PMID:11606566 in the nucleus HsPI3K-C2alpha is enriched at distinct subnuclear domains known as nuclear speckles |
| GO:0005654 nucleoplasm | ISO GO_REF:0000121 | KEEP AS NON CORE | Summary: ISO from human O00443 (HPA IDA): nucleoplasm. Reason: Human PI3K-C2alpha is enriched in nuclear speckles, which are nucleoplasmic domains, so nucleoplasm is consistent with the ortholog data; the nuclear pool is peripheral to the core trafficking function. Supporting Evidence: PMID:11606566 in the nucleus HsPI3K-C2alpha is enriched at distinct subnuclear domains known as nuclear speckles |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | MODIFY | Summary: IBA: cytoplasm (is_active_in) from the PI3K/PI4K family node. Reason: Cytoplasm is true but uninformative for a protein whose established sites of action are clathrin-coated structures and the trans-Golgi network. The row is refined to the specific cytoplasmic compartments the gene already carries (clathrin-coated vesicle, trans-Golgi network), both is_a/part_of descendants of cytoplasm. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000005673 SUPPORTS TRANSFER Family-wide node; cytoplasm is true for all PI3K/PI4K members, so the transfer is sound but stops at a general compartment. Proposed replacements: clathrin-coated vesicle trans-Golgi network Supporting Evidence: PMID:10766823 Centrifugation of rat brain homogenates and Western blotting revealed that in contrast to the class IA PI3K enzymes, PI3K-C2alpha could be co-purified with a population of clathrin-coated vesicles (CCVs) PMID:10766823 the distribution of PI3K-C2alpha closely paralleled that of gamma-adaptin, a component of the AP-1 adaptor that is present in the trans-Golgi and the trans-Golgi network (TGN) resident protein TGN-46 |
| GO:0005737 cytoplasm | ISO GO_REF:0000121 | MODIFY | Summary: ISO from human O00443: cytoplasm. Reason: Cytoplasm is true but uninformative for a protein whose established sites of action are clathrin-coated structures and the trans-Golgi network. The row is refined to the specific cytoplasmic compartments the gene already carries (clathrin-coated vesicle, trans-Golgi network), both is_a/part_of descendants of cytoplasm. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: UniProtKB:O00443 SUPPORTS TRANSFER Human donor rows (EXP PMID:11606566, PMID:14563213; IDA PMID:21081650) support cytoplasmic localisation; the specific compartments are captured by other rows. Proposed replacements: clathrin-coated vesicle trans-Golgi network Supporting Evidence: PMID:10766823 Centrifugation of rat brain homogenates and Western blotting revealed that in contrast to the class IA PI3K enzymes, PI3K-C2alpha could be co-purified with a population of clathrin-coated vesicles (CCVs) PMID:10766823 the distribution of PI3K-C2alpha closely paralleled that of gamma-adaptin, a component of the AP-1 adaptor that is present in the trans-Golgi and the trans-Golgi network (TGN) resident protein TGN-46 PMID:11606566 Homo sapiens phosphoinositide 3-kinase C2alpha (HsPI3K-C2alpha) has dual cellular localization present in the cytoplasm and in the nucleus |
| GO:0005737 cytoplasm | ISS GO_REF:0000024 | MODIFY | Summary: ISS from human O00443: cytoplasm. Reason: Cytoplasm is true but uninformative for a protein whose established sites of action are clathrin-coated structures and the trans-Golgi network. The row is refined to the specific cytoplasmic compartments the gene already carries (clathrin-coated vesicle, trans-Golgi network), both is_a/part_of descendants of cytoplasm. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: UniProtKB:O00443 SUPPORTS TRANSFER Human donor rows (EXP PMID:11606566, PMID:14563213; IDA PMID:21081650) support cytoplasmic localisation; the specific compartments are captured by other rows. Proposed replacements: clathrin-coated vesicle trans-Golgi network Supporting Evidence: PMID:10766823 Centrifugation of rat brain homogenates and Western blotting revealed that in contrast to the class IA PI3K enzymes, PI3K-C2alpha could be co-purified with a population of clathrin-coated vesicles (CCVs) PMID:10766823 the distribution of PI3K-C2alpha closely paralleled that of gamma-adaptin, a component of the AP-1 adaptor that is present in the trans-Golgi and the trans-Golgi network (TGN) resident protein TGN-46 PMID:11606566 Homo sapiens phosphoinositide 3-kinase C2alpha (HsPI3K-C2alpha) has dual cellular localization present in the cytoplasm and in the nucleus |
| GO:0005794 Golgi apparatus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (trans-Golgi network) rolled up to Golgi apparatus. Reason: Root organelle term (projects/ORGANELLES.md). The source is the UniProt location "Golgi apparatus, trans-Golgi network", and the TGN localisation is supported by co-distribution with AP-1 gamma-adaptin and TGN-46 for PI3K-C2alpha, so the organelle claim holds. The TGN sub-compartment is already carried as its own row. Supporting Evidence: PMID:10766823 the distribution of PI3K-C2alpha closely paralleled that of gamma-adaptin, a component of the AP-1 adaptor that is present in the trans-Golgi and the trans-Golgi network (TGN) resident protein TGN-46 |
| GO:0005802 trans-Golgi network | ISO GO_REF:0000121 | ACCEPT | Summary: ISO from human O00443 (IDA PMID:10766823, PMID:11239472): trans-Golgi network. Reason: PI3K-C2alpha concentrates in the TGN with AP-1 and regulates clathrin-dependent sorting from the TGN; a core location of its clathrin-associated activity. Supporting Evidence: PMID:10766823 the distribution of PI3K-C2alpha closely paralleled that of gamma-adaptin, a component of the AP-1 adaptor that is present in the trans-Golgi and the trans-Golgi network (TGN) resident protein TGN-46 PMID:11239472 clathrin functions as an adaptor for the class II PI 3-kinase C2alpha (PI3K-C2alpha), binding to its N-terminal region and stimulating its catalytic activity, especially toward phosphorylated inositide substrates |
| GO:0005829 cytosol | ISO GO_REF:0000121 | KEEP AS NON CORE | Summary: ISO from human O00443 (HPA IDA): cytosol. Reason: A soluble pool of PI3K-C2alpha exists before recruitment to membranes (e.g. PM recruitment on insulin stimulation), so cytosol is plausible, but activity is exerted on membranes. Supporting Evidence: PMID:17644513 activation of PI3K-C2alpha involves its recruitment to the plasma membrane |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: plasma membrane. Reason: PI3K-C2alpha is recruited to the plasma membrane (PX-domain binding to PI(4,5)P2, TC10-dependent recruitment on insulin stimulation) and concentrates at clathrin-coated pits where it makes PI(3,4)P2. Plasma membrane is a core location; the coated-pit sub-location is added as a NEW row. Supporting Evidence: PMID:17644513 activation of PI3K-C2alpha involves its recruitment to the plasma membrane PMID:11239472 endogenous PI3K-C2alpha is localized in coated pits PMID:17038310 the PI3K-C2alpha PX domain interacts with PtdIns(4,5)P(2)-containing membranes and thereby mediates the membrane recruitment of PI3K-C2alpha |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: IEA: plasma membrane. Reason: PI3K-C2alpha is recruited to the plasma membrane (PX-domain binding to PI(4,5)P2, TC10-dependent recruitment on insulin stimulation) and concentrates at clathrin-coated pits where it makes PI(3,4)P2. Plasma membrane is a core location; the coated-pit sub-location is added as a NEW row. Supporting Evidence: PMID:17644513 activation of PI3K-C2alpha involves its recruitment to the plasma membrane PMID:11239472 endogenous PI3K-C2alpha is localized in coated pits PMID:17038310 the PI3K-C2alpha PX domain interacts with PtdIns(4,5)P(2)-containing membranes and thereby mediates the membrane recruitment of PI3K-C2alpha |
| GO:0005886 plasma membrane | ISO GO_REF:0000121 | ACCEPT | Summary: ISO: plasma membrane. Reason: PI3K-C2alpha is recruited to the plasma membrane (PX-domain binding to PI(4,5)P2, TC10-dependent recruitment on insulin stimulation) and concentrates at clathrin-coated pits where it makes PI(3,4)P2. Plasma membrane is a core location; the coated-pit sub-location is added as a NEW row. Supporting Evidence: PMID:17644513 activation of PI3K-C2alpha involves its recruitment to the plasma membrane PMID:11239472 endogenous PI3K-C2alpha is localized in coated pits PMID:17038310 the PI3K-C2alpha PX domain interacts with PtdIns(4,5)P(2)-containing membranes and thereby mediates the membrane recruitment of PI3K-C2alpha |
| GO:0005886 plasma membrane | ISS GO_REF:0000024 | ACCEPT | Summary: ISS: plasma membrane. Reason: PI3K-C2alpha is recruited to the plasma membrane (PX-domain binding to PI(4,5)P2, TC10-dependent recruitment on insulin stimulation) and concentrates at clathrin-coated pits where it makes PI(3,4)P2. Plasma membrane is a core location; the coated-pit sub-location is added as a NEW row. Supporting Evidence: PMID:17644513 activation of PI3K-C2alpha involves its recruitment to the plasma membrane PMID:11239472 endogenous PI3K-C2alpha is localized in coated pits PMID:17038310 the PI3K-C2alpha PX domain interacts with PtdIns(4,5)P(2)-containing membranes and thereby mediates the membrane recruitment of PI3K-C2alpha |
| GO:0006897 endocytosis | ISO GO_REF:0000121 | MODIFY | Summary: ISO from human O00443: endocytosis. Reason: Endocytosis is correct but general. The best-characterised role of PI3K-C2alpha is in clathrin-mediated endocytosis, where it synthesises PI(3,4)P2 at late-stage coated pits needed for SNX9 recruitment and pit maturation, so the enzyme performs a step of the process. The row is refined to clathrin-dependent endocytosis (an is_a descendant of endocytosis). The donor IMP (PMID:21081650) concerned dynamin-independent uptake, which is real but less mechanistically resolved; it remains covered by the parent if other rows retain it. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: UniProtKB:O00443 SUPPORTS TRANSFER Human IMP (PMID:21081650) on dynamin-independent internalisation; clathrin-mediated roles shown in PMID:11239472 and PMID:23823722. Proposed replacements: clathrin-dependent endocytosis Supporting Evidence: PMID:23823722 formation of phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) by class II phosphatidylinositol-3-kinase C2Ξ± (PI(3)K C2Ξ±) spatiotemporally controls clathrin-mediated endocytosis PMID:23823722 Depletion of PI(3,4)P2 or PI(3)K C2Ξ± impairs the maturation of late-stage clathrin-coated pits before fission. PMID:21081650 downregulation of PI3KC2Ξ± impaired internalization of CD59 as well as fluid-phase endocytosis |
| GO:0006897 endocytosis | ISS GO_REF:0000024 | MODIFY | Summary: ISS from human O00443: endocytosis. Reason: Endocytosis is correct but general. The best-characterised role of PI3K-C2alpha is in clathrin-mediated endocytosis, where it synthesises PI(3,4)P2 at late-stage coated pits needed for SNX9 recruitment and pit maturation, so the enzyme performs a step of the process. The row is refined to clathrin-dependent endocytosis (an is_a descendant of endocytosis). The donor IMP (PMID:21081650) concerned dynamin-independent uptake, which is real but less mechanistically resolved; it remains covered by the parent if other rows retain it. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: UniProtKB:O00443 SUPPORTS TRANSFER Human IMP (PMID:21081650) on dynamin-independent internalisation; clathrin-mediated roles shown in PMID:11239472 and PMID:23823722. Proposed replacements: clathrin-dependent endocytosis Supporting Evidence: PMID:23823722 formation of phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) by class II phosphatidylinositol-3-kinase C2Ξ± (PI(3)K C2Ξ±) spatiotemporally controls clathrin-mediated endocytosis PMID:23823722 Depletion of PI(3,4)P2 or PI(3)K C2Ξ± impairs the maturation of late-stage clathrin-coated pits before fission. PMID:21081650 downregulation of PI3KC2Ξ± impaired internalization of CD59 as well as fluid-phase endocytosis |
| GO:0008150 biological_process | ND GO_REF:0000015 | REMOVE | Summary: ND placeholder for biological process. Reason: An ND root-term annotation is no longer accurate: PI3K-C2alpha has well-characterised processes (PI3P synthesis, clathrin-mediated endocytosis), with rat-cell evidence in insulin granule exocytosis. The placeholder adds nothing. Supporting Evidence: PMID:21127054 Here we report that selective down-regulation of this PI3K isoform in INS1 rat insulinoma cells specifically impairs insulin secretion irrespective of the metabolic effect, without affecting insulin content or the number of insulin granules associated with the plasma membrane in resting cells. PMID:23823722 formation of phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) by class II phosphatidylinositol-3-kinase C2Ξ± (PI(3)K C2Ξ±) spatiotemporally controls clathrin-mediated endocytosis |
| GO:0009267 cellular response to starvation | ISO GO_REF:0000121 | MARK AS OVER ANNOTATED | Summary: ISO from mouse (IGI PMID:24098492): cellular response to starvation (acts_upstream_of_or_within). Reason: The donor experiment silenced PI3K-C2alpha and PI3K-C2beta together in MEFs, so the starvation phenotype cannot be attributed to C2alpha alone, and Vps34 is the main PI3P source in starvation-induced autophagy. In kidney epithelia PIK3C2A supplies PI3P for shear-stress, not starvation, autophagy. Response to starvation as a whole over-reaches what was shown; the autophagy contribution is captured by the macroautophagy and autophagy-regulation rows. Propagation Review Root cause: SOURCE WEAK OR INFERRED Failure modes: SOURCE EVIDENCE WEAK Sources checked: MGI:MGI:1203729 SOURCE WEAK OR INFERRED Mouse IGI from combined alpha+beta class II siRNA (PMID:24098492); not specific to Pik3c2a. Supporting Evidence: PMID:24098492 Control and Vps34 KO cells were treated with mock siRNA or both PI3K-C2Ξ± and Ξ² siRNAs PMID:32102612 We showed that PtdIns3P is generated by PIK3C2A, but not by PIK3C3/VPS34, during flow-associated primary cilium-dependent autophagy, in a ULK1-independent manner. |
| GO:0010508 positive regulation of autophagy | ISO GO_REF:0000121 | KEEP AS NON CORE | Summary: ISO from human O00443 (IMP PMID:28910396): positive regulation of autophagy. Reason: PIK3C2A knockdown reduces autophagy in U2OS cells, rescued by wild-type but not kinase-dead enzyme, and PIK3C2A provides PI3P for cilium-dependent autophagy. True, kinase-dependent, but a context-specific output of its PI3P production rather than its core trafficking role. Supporting Evidence: PMID:28910396 This defective autophagy is rescued by exogenous PI3K-C2Ξ±, but not kinase-dead PI3K-C2Ξ±. PMID:32102612 We showed that PtdIns3P is generated by PIK3C2A, but not by PIK3C3/VPS34, during flow-associated primary cilium-dependent autophagy, in a ULK1-independent manner. |
| GO:0016236 macroautophagy | ISO GO_REF:0000121 | KEEP AS NON CORE | Summary: ISO from mouse (IGI PMID:24098492): macroautophagy (acts_upstream_of_or_within). Reason: Class II PI3Ks contribute a Vps34-independent PI3P pool to autophagosome biogenesis, and PIK3C2A is the PI3P source for shear-stress autophagy; the kinase-dead rescue failure in human cells supports a direct catalytic contribution. Non-core relative to endocytic trafficking. Supporting Evidence: PMID:24098492 class II PI3Ks also significantly contribute to PI3P generation and regulate AP biogenesis PMID:28910396 This defective autophagy is rescued by exogenous PI3K-C2Ξ±, but not kinase-dead PI3K-C2Ξ±. PMID:32102612 We showed that PtdIns3P is generated by PIK3C2A, but not by PIK3C3/VPS34, during flow-associated primary cilium-dependent autophagy, in a ULK1-independent manner. |
| GO:0016301 kinase activity | IEA GO_REF:0000120 | MODIFY | Summary: IEA (InterPro/UniRule): kinase activity. Reason: Kinase activity is correct but uninformative; the specific lipid kinase activities (1-phosphatidylinositol-3-kinase and 1-phosphatidylinositol-4-phosphate 3-kinase activity, both is_a descendants) are already carried by this gene and supported by ortholog data. Proposed replacements: 1-phosphatidylinositol-3-kinase activity 1-phosphatidylinositol-4-phosphate 3-kinase activity Supporting Evidence: file:rat/Pik3c2a/Pik3c2a-uniprot.txt IPR037705; PI3-kinase_C2-alpha_cat PMID:9337861 the enzyme only phosphorylates PtdIns and PtdIns4P when the lipids are presented alone |
| GO:0016303 1-phosphatidylinositol-3-kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: 1-phosphatidylinositol-3-kinase activity. Reason: PI3K-C2alpha phosphorylates PtdIns to PtdIns3P in vitro and in vivo (sole insulin-stimulated product in muscle cells) and generates PI3P pools at recycling endosomes, autophagosome precursors and secretory granules. The rat protein carries the class II alpha catalytic domain with an intact catalytic loop; ortholog transfer is sound. Core activity. Supporting Evidence: PMID:9337861 the enzyme only phosphorylates PtdIns and PtdIns4P when the lipids are presented alone PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha file:rat/Pik3c2a/Pik3c2a-uniprot.txt IPR037705; PI3-kinase_C2-alpha_cat |
| GO:0016303 1-phosphatidylinositol-3-kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA: 1-phosphatidylinositol-3-kinase activity. Reason: PI3K-C2alpha phosphorylates PtdIns to PtdIns3P in vitro and in vivo (sole insulin-stimulated product in muscle cells) and generates PI3P pools at recycling endosomes, autophagosome precursors and secretory granules. The rat protein carries the class II alpha catalytic domain with an intact catalytic loop; ortholog transfer is sound. Core activity. Supporting Evidence: PMID:9337861 the enzyme only phosphorylates PtdIns and PtdIns4P when the lipids are presented alone PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha file:rat/Pik3c2a/Pik3c2a-uniprot.txt IPR037705; PI3-kinase_C2-alpha_cat file:rat/Pik3c2a/Pik3c2a-deep-research-manual.md DFG motif (residue 1269) are present in the rat sequence |
| GO:0016303 1-phosphatidylinositol-3-kinase activity | ISO GO_REF:0000121 | ACCEPT | Summary: ISO (mouse): 1-phosphatidylinositol-3-kinase activity. Reason: PI3K-C2alpha phosphorylates PtdIns to PtdIns3P in vitro and in vivo (sole insulin-stimulated product in muscle cells) and generates PI3P pools at recycling endosomes, autophagosome precursors and secretory granules. The rat protein carries the class II alpha catalytic domain with an intact catalytic loop; ortholog transfer is sound. Core activity. Supporting Evidence: PMID:9337861 the enzyme only phosphorylates PtdIns and PtdIns4P when the lipids are presented alone PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha file:rat/Pik3c2a/Pik3c2a-uniprot.txt IPR037705; PI3-kinase_C2-alpha_cat |
| GO:0016303 1-phosphatidylinositol-3-kinase activity | ISO GO_REF:0000121 | ACCEPT | Summary: ISO (human): 1-phosphatidylinositol-3-kinase activity. Reason: PI3K-C2alpha phosphorylates PtdIns to PtdIns3P in vitro and in vivo (sole insulin-stimulated product in muscle cells) and generates PI3P pools at recycling endosomes, autophagosome precursors and secretory granules. The rat protein carries the class II alpha catalytic domain with an intact catalytic loop; ortholog transfer is sound. Core activity. Supporting Evidence: PMID:9337861 the enzyme only phosphorylates PtdIns and PtdIns4P when the lipids are presented alone PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha file:rat/Pik3c2a/Pik3c2a-uniprot.txt IPR037705; PI3-kinase_C2-alpha_cat |
| GO:0016477 cell migration | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA: cell migration. Reason: PI3K-C2alpha knockdown impairs endothelial and smooth-muscle cell migration, but this is a downstream consequence of defective endosomal trafficking and receptor/RhoA signalling, not participation in the migration machinery. The IBA node (PTN000005674) spans class I and class II PI3Ks; for C2alpha the regulatory relation is better captured by the positive regulation of cell migration row. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: PANTHER:PTN000005674 SUPPORTS SOURCE BUT NOT TARGET Node seeded by fly, zebrafish and other PI3K data; for PI3K-C2alpha the evidence is indirect (trafficking defects causing migration defects). Supporting Evidence: PMID:22983395 PI3K-C2Ξ± knockdown in endothelial cells resulted in a decrease in the number of PI3-phosphate-enriched endosomes, impaired endosomal trafficking PMID:22983395 Together, the effects of PI3K-C2Ξ± knockdown led to defective endothelial cell migration, proliferation, tube formation and barrier integrity. |
| GO:0016740 transferase activity | IEA GO_REF:0000104 | MODIFY | Summary: IEA (UniRule): transferase activity. Reason: Transferase activity is correct but uninformative; refine to the specific phosphatidylinositol 3-kinase activities already carried by the gene (is_a descendants). Proposed replacements: 1-phosphatidylinositol-3-kinase activity 1-phosphatidylinositol-4-phosphate 3-kinase activity Supporting Evidence: file:rat/Pik3c2a/Pik3c2a-uniprot.txt IPR037705; PI3-kinase_C2-alpha_cat PMID:9337861 the enzyme only phosphorylates PtdIns and PtdIns4P when the lipids are presented alone |
| GO:0030136 clathrin-coated vesicle | IEA GO_REF:0000044 | ACCEPT | Summary: IEA (UniProt subcellular location): clathrin-coated vesicle. Reason: PI3K-C2alpha co-purifies with clathrin-coated vesicles from rat brain, the only class of PI3K to do so, and wortmannin-resistant PI3K activity is present in CCV preparations. Direct rat-tissue support for a core location. Supporting Evidence: PMID:10766823 Centrifugation of rat brain homogenates and Western blotting revealed that in contrast to the class IA PI3K enzymes, PI3K-C2alpha could be co-purified with a population of clathrin-coated vesicles (CCVs) |
| GO:0030136 clathrin-coated vesicle | ISO GO_REF:0000121 | ACCEPT | Summary: ISO from human O00443 (IDA PMID:10766823, PMID:11239472): clathrin-coated vesicle. Reason: Supported by rat-brain CCV co-purification in the donor paper itself; core location. Supporting Evidence: PMID:10766823 Centrifugation of rat brain homogenates and Western blotting revealed that in contrast to the class IA PI3K enzymes, PI3K-C2alpha could be co-purified with a population of clathrin-coated vesicles (CCVs) |
| GO:0030276 clathrin binding | ISO GO_REF:0000121 | ACCEPT | Summary: ISO from human O00443 (IDA PMID:11239472): clathrin binding. Reason: Clathrin binds the PI3K-C2alpha N-terminus, activates the kinase, and the clathrin-binding domain alone drives clathrin lattice assembly. A core molecular function coupling the enzyme to clathrin-coated membranes. Supporting Evidence: PMID:11239472 clathrin functions as an adaptor for the class II PI 3-kinase C2alpha (PI3K-C2alpha), binding to its N-terminal region and stimulating its catalytic activity, especially toward phosphorylated inositide substrates PMID:16215232 the isolated clathrin binding domain of PI3K-C2alpha can drive clathrin lattice assembly |
| GO:0031982 vesicle | ISO GO_REF:0000121 | MODIFY | Summary: ISO from human O00443: vesicle. Reason: Vesicle is correct but general; the donor IDA (PMID:21081650) observed PI3KC2alpha on cargo-positive endocytic vesicles, and the best-defined vesicular location is clathrin-coated vesicles (rat brain CCV fractionation). Refine to clathrin-coated vesicle, an is_a descendant already carried by the gene. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: UniProtKB:O00443 SUPPORTS TRANSFER Human IDA (PMID:21081650) on cargo-positive vesicles; transfer sound, granularity coarse. Proposed replacements: clathrin-coated vesicle Supporting Evidence: PMID:21081650 a relocalization of PI3KC2Ξ± to cargo-positive vesicles PMID:10766823 Centrifugation of rat brain homogenates and Western blotting revealed that in contrast to the class IA PI3K enzymes, PI3K-C2alpha could be co-purified with a population of clathrin-coated vesicles (CCVs) |
| GO:0031982 vesicle | ISS GO_REF:0000024 | MODIFY | Summary: ISS from human O00443: vesicle. Reason: Vesicle is correct but general; the donor IDA (PMID:21081650) observed PI3KC2alpha on cargo-positive endocytic vesicles, and the best-defined vesicular location is clathrin-coated vesicles (rat brain CCV fractionation). Refine to clathrin-coated vesicle, an is_a descendant already carried by the gene. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: UniProtKB:O00443 SUPPORTS TRANSFER Human IDA (PMID:21081650) on cargo-positive vesicles; transfer sound, granularity coarse. Proposed replacements: clathrin-coated vesicle Supporting Evidence: PMID:21081650 a relocalization of PI3KC2Ξ± to cargo-positive vesicles PMID:10766823 Centrifugation of rat brain homogenates and Western blotting revealed that in contrast to the class IA PI3K enzymes, PI3K-C2alpha could be co-purified with a population of clathrin-coated vesicles (CCVs) |
| GO:0035005 1-phosphatidylinositol-4-phosphate 3-kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: 1-phosphatidylinositol-4-phosphate 3-kinase activity. Reason: Class II PI3K-C2alpha uses PtdIns4P as a preferred substrate in vitro (stimulated by clathrin) and produces PI(3,4)P2 at late-stage clathrin-coated pits, where the lipid recruits SNX9 and drives pit maturation. Core activity alongside PI 3-kinase activity. Supporting Evidence: PMID:9337861 the enzyme only phosphorylates PtdIns and PtdIns4P when the lipids are presented alone PMID:11239472 clathrin functions as an adaptor for the class II PI 3-kinase C2alpha (PI3K-C2alpha), binding to its N-terminal region and stimulating its catalytic activity, especially toward phosphorylated inositide substrates PMID:23823722 formation of phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) by class II phosphatidylinositol-3-kinase C2Ξ± (PI(3)K C2Ξ±) spatiotemporally controls clathrin-mediated endocytosis |
| GO:0035005 1-phosphatidylinositol-4-phosphate 3-kinase activity | IEA GO_REF:0000003 | ACCEPT | Summary: IEA (EC 2.7.1.154): 1-phosphatidylinositol-4-phosphate 3-kinase activity. Reason: Class II PI3K-C2alpha uses PtdIns4P as a preferred substrate in vitro (stimulated by clathrin) and produces PI(3,4)P2 at late-stage clathrin-coated pits, where the lipid recruits SNX9 and drives pit maturation. Core activity alongside PI 3-kinase activity. Supporting Evidence: PMID:9337861 the enzyme only phosphorylates PtdIns and PtdIns4P when the lipids are presented alone PMID:11239472 clathrin functions as an adaptor for the class II PI 3-kinase C2alpha (PI3K-C2alpha), binding to its N-terminal region and stimulating its catalytic activity, especially toward phosphorylated inositide substrates PMID:23823722 formation of phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) by class II phosphatidylinositol-3-kinase C2Ξ± (PI(3)K C2Ξ±) spatiotemporally controls clathrin-mediated endocytosis |
| GO:0035005 1-phosphatidylinositol-4-phosphate 3-kinase activity | ISO GO_REF:0000121 | ACCEPT | Summary: ISO (human): 1-phosphatidylinositol-4-phosphate 3-kinase activity. Reason: Class II PI3K-C2alpha uses PtdIns4P as a preferred substrate in vitro (stimulated by clathrin) and produces PI(3,4)P2 at late-stage clathrin-coated pits, where the lipid recruits SNX9 and drives pit maturation. Core activity alongside PI 3-kinase activity. Supporting Evidence: PMID:9337861 the enzyme only phosphorylates PtdIns and PtdIns4P when the lipids are presented alone PMID:11239472 clathrin functions as an adaptor for the class II PI 3-kinase C2alpha (PI3K-C2alpha), binding to its N-terminal region and stimulating its catalytic activity, especially toward phosphorylated inositide substrates PMID:23823722 formation of phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) by class II phosphatidylinositol-3-kinase C2Ξ± (PI(3)K C2Ξ±) spatiotemporally controls clathrin-mediated endocytosis |
| GO:0035091 phosphatidylinositol binding | IEA GO_REF:0000002 | MODIFY | Summary: IEA (InterPro PX domain): phosphatidylinositol binding. Reason: Correct but general. The PI3K-C2alpha PX domain has a PI-binding site optimised for PI(4,5)P2 and mediates membrane recruitment through PI(4,5)P2; refine to phosphatidylinositol-4,5-bisphosphate binding (an is_a descendant via phosphatidylinositol phosphate binding). Proposed replacements: phosphatidylinositol-4,5-bisphosphate binding Supporting Evidence: PMID:17038310 This PX domain contains a signature PI-binding site that is optimized for PtdIns(4,5)P(2) binding. PMID:17038310 the PI3K-C2alpha PX domain interacts with PtdIns(4,5)P(2)-containing membranes and thereby mediates the membrane recruitment of PI3K-C2alpha file:rat/Pik3c2a/Pik3c2a-uniprot.txt IPR042133; PX_PI3K_C2_alpha |
| GO:0036092 phosphatidylinositol-3-phosphate biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: phosphatidylinositol-3-phosphate biosynthetic process. Reason: PI3K-C2alpha produces PI3P in vivo (insulin-stimulated, recycling endosome, autophagy, secretory granule pools); the MF 1-phosphatidylinositol-3-kinase activity is part_of this process. Core. Supporting Evidence: PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha PMID:24697898 PI3K-C2Ξ± is enriched in the pericentriolar recycling endocytic compartment (PRE) at the base of the primary cilium, where it regulates production of a specific pool of PtdIns3P. PMID:32102612 We showed that PtdIns3P is generated by PIK3C2A, but not by PIK3C3/VPS34, during flow-associated primary cilium-dependent autophagy, in a ULK1-independent manner. |
| GO:0036092 phosphatidylinositol-3-phosphate biosynthetic process | ISO GO_REF:0000121 | ACCEPT | Summary: ISO from mouse (IGI PMID:24098492): phosphatidylinositol-3-phosphate biosynthetic process (acts_upstream_of_or_within). Reason: Same claim as the IBA row; mouse data show class II PI3Ks contribute a Vps34-independent PI3P pool, and C2alpha-specific PI3P production is shown elsewhere. Supporting Evidence: PMID:24098492 class II PI3Ks also significantly contribute to PI3P generation and regulate AP biogenesis PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha |
| GO:0043491 phosphatidylinositol 3-kinase/protein kinase B signal transduction | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA: phosphatidylinositol 3-kinase/protein kinase B signal transduction. Reason: The IBA donors are dominated by class I PI3Ks (PIK3CA, PIK3CB, PIK3CD, PIK3CG) that make PIP3 to activate PKB/Akt. PI3K-C2alpha mainly makes PI3P and PI(3,4)P2; in INS1 cells its effect on secretion is Akt-independent. A beta-cell knockdown study links it to IR-B/PKB signalling, so a contextual contribution is possible, but PI3K/PKB signal transduction is not a general function of this enzyme. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000005674 SUPPORTS SOURCE BUT NOT TARGET Node covers class I and II PI3Ks; the PKB-signalling claim rests on class I donors whose PIP3 product class II alpha does not normally generate. Supporting Evidence: PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha PMID:21127054 These data indicate that activation of the insulin receptor and Akt do not play a key role in the KCl-dependent insulin secretion in our experimental conditions. PMID:26387957 knockdown of PI3K-C2Ξ± expression results in rerouting of the insulin signal from insulin receptor (IR)-B/PI3K-C2Ξ±/PKB-mediated metabolic signaling to IR-B/Shc/ERK-mediated mitogenic signaling |
| GO:0046854 phosphatidylinositol phosphate biosynthetic process | IEA GO_REF:0000002 | MODIFY | Summary: IEA (InterPro PI3/4 kinase family): phosphatidylinositol phosphate biosynthetic process. Reason: Correct but general; refine to phosphatidylinositol-3-phosphate biosynthetic process (is_a descendant), which the gene already carries by IBA and ISO. Proposed replacements: phosphatidylinositol-3-phosphate biosynthetic process Supporting Evidence: PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha file:rat/Pik3c2a/Pik3c2a-uniprot.txt IPR037705; PI3-kinase_C2-alpha_cat |
| GO:0046934 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity | IEA GO_REF:0000003 | MARK AS OVER ANNOTATED | Summary: IEA (EC 2.7.1.153): 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity. Reason: Recombinant PI3K-C2alpha phosphorylates PtdIns(4,5)P2 only when the lipid is presented with phosphatidylserine as carrier, and clathrin stimulates activity toward phosphorylated inositides; in cells the identified products are PI3P and PI(3,4)P2, not PIP3. The in vitro activity is not entirely wrong, but as an annotation it overstates a minor carrier-dependent side activity. The PANTHER PTHR10048 family review likewise scopes this activity to the class I catalytic subunits only, which excludes this class II enzyme. Supporting Evidence: PMID:9337861 when lipids were presented together with phosphatidylserine acting as a carrier, phosphorylation of PtdIns(4,5)P2 was also observed PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha |
| GO:0046934 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity | ISO GO_REF:0000121 | MARK AS OVER ANNOTATED | Summary: ISO (human IDA): 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity. Reason: Recombinant PI3K-C2alpha phosphorylates PtdIns(4,5)P2 only when the lipid is presented with phosphatidylserine as carrier, and clathrin stimulates activity toward phosphorylated inositides; in cells the identified products are PI3P and PI(3,4)P2, not PIP3. The in vitro activity is not entirely wrong, but as an annotation it overstates a minor carrier-dependent side activity. The PANTHER PTHR10048 family review likewise scopes this activity to the class I catalytic subunits only, which excludes this class II enzyme. Propagation Review Root cause: SOURCE WEAK OR INFERRED Failure modes: SOURCE EVIDENCE WEAK Sources checked: UniProtKB:O00443 SOURCE WEAK OR INFERRED The human IDA rests on in vitro PtdIns(4,5)P2 phosphorylation that needs a phosphatidylserine carrier; the in vivo products are PI3P and PI(3,4)P2. Supporting Evidence: PMID:9337861 when lipids were presented together with phosphatidylserine acting as a carrier, phosphorylation of PtdIns(4,5)P2 was also observed PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha |
| GO:0048015 phosphatidylinositol-mediated signaling | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA: phosphatidylinositol-mediated signaling. Reason: PI3K-C2alpha generates phosphoinositide second messengers (PI3P, PI(3,4)P2) that recruit effectors such as SNX9 and WIPI proteins and act downstream of insulin and other receptors; participation in phosphatidylinositol-mediated signalling is reasonable but peripheral to its trafficking role. Supporting Evidence: PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha PMID:23823722 formation of phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) by class II phosphatidylinositol-3-kinase C2Ξ± (PI(3)K C2Ξ±) spatiotemporally controls clathrin-mediated endocytosis |
| GO:0048015 phosphatidylinositol-mediated signaling | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: IEA (UniRule): phosphatidylinositol-mediated signaling. Reason: PI3K-C2alpha generates phosphoinositide second messengers (PI3P, PI(3,4)P2) that recruit effectors such as SNX9 and WIPI proteins and act downstream of insulin and other receptors; participation in phosphatidylinositol-mediated signalling is reasonable but peripheral to its trafficking role. Supporting Evidence: PMID:17644513 we here identify phosphatidylinositol 3-phosphate as the sole in vivo product of the insulin-dependent activation of PI3K-C2alpha PMID:23823722 formation of phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) by class II phosphatidylinositol-3-kinase C2Ξ± (PI(3)K C2Ξ±) spatiotemporally controls clathrin-mediated endocytosis |
| GO:0071583 negative regulation of zinc ion transmembrane transport | ISO GO_REF:0000121 | UNDECIDED | Summary: ISO from mouse (IMP PMID:23823722): negative regulation of zinc ion transmembrane transport (acts_upstream_of_or_within). Reason: The mouse donor annotation cites Posor et al. 2013, whose abstract concerns PI(3,4)P2 synthesis by PI3K-C2alpha in clathrin-mediated endocytosis and does not mention zinc. The full text is not available here, so the basis for a zinc-transport claim cannot be checked; it may be a mis-keyed term or reference. No other evidence links PI3K-C2alpha to zinc transport. Propagation Review Root cause: UNRESOLVED Sources checked: MGI:MGI:1203729 UNRESOLVED Mouse IMP to GO:0071583 citing PMID:23823722; abstract does not support zinc transport, full text not read. Supporting Evidence: PMID:23823722 formation of phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) by class II phosphatidylinositol-3-kinase C2Ξ± (PI(3)K C2Ξ±) spatiotemporally controls clathrin-mediated endocytosis |
| GO:0090050 positive regulation of cell migration involved in sprouting angiogenesis | ISO GO_REF:0000121 | KEEP AS NON CORE | Summary: ISO from human O00443 (IMP PMID:26175229): positive regulation of cell migration involved in sprouting angiogenesis. Reason: The donor is a miR-206 study in endothelial progenitor cells, which is indirect, but endothelial knockout/knockdown of PI3K-C2alpha shows defective sprouting angiogenesis and endothelial cell migration through impaired endosomal trafficking and VEGFR/RhoA signalling. A regulatory role in endothelial migration during sprouting angiogenesis is supported for the mammalian ortholog; it is a tissue context, not the core function. Supporting Evidence: PMID:26175229 MiR-206 was found to regulate endothelial progenitor cell activities by targeting the protein kinase PIK3C2Ξ± PMID:22983395 Global or endothelial-cell-specific deficiency of PI3K-C2Ξ± resulted in embryonic lethality caused by defects in sprouting angiogenesis and vascular maturation. PMID:22983395 Together, the effects of PI3K-C2Ξ± knockdown led to defective endothelial cell migration, proliferation, tube formation and barrier integrity. |
| GO:1905037 autophagosome organization | ISO GO_REF:0000121 | KEEP AS NON CORE | Summary: ISO from mouse (IGI PMID:24098492): autophagosome organization (acts_upstream_of_or_within). Reason: Class II PI3K-derived PI3P supports WIPI-1 and LC3 recruitment to autophagosome nucleation sites; PIK3C2A provides PI3P for cilium-dependent autophagosome formation. A real, non-core contribution. Supporting Evidence: PMID:24098492 class II PI3Ks also significantly contribute to PI3P generation and regulate AP biogenesis PMID:32102612 We showed that PtdIns3P is generated by PIK3C2A, but not by PIK3C3/VPS34, during flow-associated primary cilium-dependent autophagy, in a ULK1-independent manner. |
| GO:0005905 clathrin-coated pit | ISS PMID:11239472 The class II phosphoinositide 3-kinase C2alpha is activated ... | NEW | Summary: Proposed: PI3K-C2alpha localises to clathrin-coated pits at the plasma membrane, where it generates PI(3,4)P2 for pit maturation. Reason: Two independent lines agree: endogenous PI3K-C2alpha is localised in coated pits (PMID:11239472), and its PI(3,4)P2 product acts on late-stage coated pits (PMID:23823722); the clathrin-binding N-terminus provides the targeting mechanism. The rat ortholog shares the domain architecture. Added beside the plasma membrane rows, not as a replacement. Supporting Evidence: PMID:11239472 endogenous PI3K-C2alpha is localized in coated pits PMID:23823722 Depletion of PI(3,4)P2 or PI(3)K C2Ξ± impairs the maturation of late-stage clathrin-coated pits before fission. PMID:11239472 clathrin functions as an adaptor for the class II PI 3-kinase C2alpha (PI3K-C2alpha), binding to its N-terminal region and stimulating its catalytic activity, especially toward phosphorylated inositide substrates |
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Download this section (compressed HTML)Q: Should RGD add a rat IMP annotation from PMID:21127054 (INS1 knockdown) to a regulation-of-insulin-secretion term, given that the mechanism (PtdIns3P-dependent granule fusion competence) is only inferred from PC12 data?
Q: What is the basis of the mouse IMP to GO:0071583 negative regulation of zinc ion transmembrane transport citing PMID:23823722, which concerns clathrin-mediated endocytosis?
Q: Which lipid product (PI3P or PI(3,4)P2) mediates PI3K-C2alpha function in insulin granule fusion, and on which membrane is it made?
Experiment: In INS1 cells depleted of endogenous PI3K-C2alpha, re-express siRNA-resistant wild-type, kinase-dead, or clathrin-binding-deficient PI3K-C2alpha and measure KCl-evoked secretion, SNAP25 proteolysis, and single-granule fusion by TIRF, with PI3P and PI(3,4)P2 biosensors to identify the lipid acting at the granule.
Hypothesis: PI3K-C2alpha catalytic activity, not only its clathrin-binding scaffold, is required for insulin granule fusion in rat beta cells.
Type: rescue with domain mutants and live-cell TIRF imaging
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