IplA is the sole inositol 1,4,5-trisphosphate/ryanodine receptor family member in Dictyostelium discoideum and the only recognizable homolog of the metazoan IP3 receptor in this organism. It is a very large (3177 aa) multi-pass endoplasmic reticulum membrane protein with a long cytoplasmic N-terminal region containing predicted InsP3-binding residues and a C-terminal six-transmembrane channel domain, and it assembles into the intracellular ligand-gated calcium-release channel that governs Ca2+ efflux from ER stores into the cytosol. Genetic ablation of iplA abolishes the chemoattractant (cAMP/folate)-stimulated Ca2+ entry and the accompanying rise in free cytosolic Ca2+, while leaving resting cytosolic Ca2+, cAMP chemotaxis, cGMP production and MAP kinase signaling intact. IplA is specifically required for chemotaxis up spatial Ca2+ gradients and contributes to a wide range of Ca2+-dependent processes, including natural aggregation, arachidonate chemotaxis, AprA-mediated chemorepulsion, mechanosensory Ca2+ bursts in slugs, regulation of blebbing, DIF-induced autophagic cell death with cellulose shell synthesis, and polyphosphate/IP3-Ca2+ feedback inhibition of proliferation. Although it is clearly a Ca2+ channel of the InsP3R/RyR family, direct biochemical demonstration that IplA is gated by InsP3 is still lacking.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0030659
cytoplasmic vesicle membrane
|
IBA
GO_REF:0000033 |
KEEP AS NON CORE |
Summary: Phylogenetic (IBA) inference placing IplA in vesicle membranes. IP3-receptor family channels reside chiefly in the ER membrane but are also found in vesicle membranes, so this is plausible but not the principal, best-supported location.
Reason: The endoplasmic reticulum membrane is the established primary location for IplA; a cytoplasmic vesicle membrane pool is plausible for an IP3R-family channel but is secondary to the core ER-membrane localization.
Supporting Evidence:
PMID:22375061
usually located in the membrane of endoplasmic reticulum and vesicles, but are also found at low levels in the plasma membrane
|
|
GO:0005220
inositol 1,4,5-trisphosphate-gated calcium channel activity
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: InterPro2GO transfer of the specific mammalian ITPR molecular function. IplA is the sole IP3R-family homolog and functions as an intracellular Ca2+-release channel, but direct biochemical evidence that it is gated by InsP3 is explicitly lacking, so the specific InsP3-gated term over-reaches what has been demonstrated.
Reason: The demonstrated activity is that of an (intracellular) calcium channel; InsP3-gating is inferred from sequence homology and conserved binding residues but has not been shown biochemically. Generalizing the overly specific InsP3-gated term to calcium channel activity better matches the evidence.
Proposed replacements:
calcium channel activity
Supporting Evidence:
PMID:10970875
biochemical evidence that IplA is an InsP 3 receptor is still lacking
PMID:40295210
IplA, a Dictyostelium protein analogous to the mammalian IP3 receptor, is a ligand-gated calcium channel responsible for calcium release from the endoplasmic reticulum
|
|
GO:0005262
calcium channel activity
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: IplA is an intracellular ligand-gated calcium-release channel; ablation of iplA abolishes chemoattractant-stimulated Ca2+ fluxes. This is the core molecular function of the gene product.
Reason: Calcium channel activity is the well-supported core function, consistent with the InsP3R/RyR family assignment and the loss of Ca2+ fluxes in iplA-null cells.
Supporting Evidence:
PMID:10970875
InsP 3 /RyR receptor family of ligand-gated Ca 2+ channels
PMID:40295210
IplA, a Dictyostelium protein analogous to the mammalian IP3 receptor, is a ligand-gated calcium channel responsible for calcium release from the endoplasmic reticulum
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000117 |
KEEP AS NON CORE |
Summary: Generic ARBA-derived cytoplasm localization. Not incorrect (the cytoplasmic N-terminal region is large) but uninformative relative to the specific ER-membrane localization.
Reason: Cytoplasm is a high-level, uninformative location for a multi-pass ER membrane channel; the endoplasmic reticulum membrane term captures the biology better.
|
|
GO:0005783
endoplasmic reticulum
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: The endoplasmic reticulum is the established compartment for IplA, consistent with its role as an ER Ca2+-store release channel.
Reason: ER localization is supported by the UniProt subcellular location and by the protein's function in releasing Ca2+ from ER stores.
Supporting Evidence:
PMID:18077554
a ligand-gated channel governing Ca(2+) efflux from endoplasmic reticulum stores
|
|
GO:0005789
endoplasmic reticulum membrane
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: The most precise and best-supported location for IplA, a multi-pass ER membrane channel that releases Ca2+ from ER stores into the cytosol.
Reason: ER membrane localization matches the UniProt subcellular location, the six-transmembrane topology, and the ER Ca2+-store release function.
Supporting Evidence:
PMID:40295210
IplA, a Dictyostelium protein analogous to the mammalian IP3 receptor, is a ligand-gated calcium channel responsible for calcium release from the endoplasmic reticulum
|
|
GO:0006816
calcium ion transport
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Calcium ion transport is a direct consequence of IplA channel activity and is central to its function.
Reason: As a Ca2+ channel, IplA mediates calcium ion transport; ablation abolishes chemoattractant-stimulated Ca2+ fluxes.
Supporting Evidence:
PMID:10970875
Ca(2+) entry in response to chemoattractants is abolished
|
|
GO:0016020
membrane
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: Generic membrane localization, subsumed by the more specific endoplasmic reticulum membrane term.
Reason: Membrane is an uninformative high-level location; the ER membrane annotation is the informative one.
|
|
GO:0070588
calcium ion transmembrane transport
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Transmembrane movement of Ca2+ across the ER membrane is the core activity of this channel.
Reason: IplA conducts Ca2+ across the ER membrane; this process directly reflects its channel function.
Supporting Evidence:
PMID:18077554
a ligand-gated channel governing Ca(2+) efflux from endoplasmic reticulum stores
|
|
GO:0070679
inositol 1,4,5 trisphosphate binding
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: InterPro2GO transfer based on the IP3R-family InsP3-binding domain. IplA retains predicted InsP3-binding residues, but direct biochemical InsP3 binding has not been demonstrated for this divergent protein.
Reason: InsP3 binding is inferred from conserved sequence features; experimental verification is lacking (biochemical evidence that IplA is an InsP3 receptor is still lacking), so it should not be treated as an established core function.
Supporting Evidence:
PMID:10970875
biochemical evidence that IplA is an InsP 3 receptor is still lacking
|
|
GO:0019722
calcium-mediated signaling
|
IMP
PMID:40295210 Intracellular Calcium Responses to External Calcium Stimuli ... |
ACCEPT |
Summary: iplA-null cells show a reduced proportion of cells mounting an intracellular Ca2+ response to external calcium, placing IplA within calcium-mediated signaling.
Reason: Directly supported by the phenotype of iplA-null cells in calcium-signaling assays; this is closely tied to the core channel function.
Supporting Evidence:
PMID:40295210
only approximately 60% of iplA-null cells were responsive to the external calcium stimuli
PMID:40295210
IplA-related signaling pathways are involved in regulating intracellular calcium levels in response to external calcium stimuli
|
|
GO:0006935
chemotaxis
|
IMP
PMID:22375061 The IplA Ca2+ channel of Dictyostelium discoideum is necessa... |
KEEP AS NON CORE |
Summary: iplA-null cells retain normal chemotaxis to cAMP but specifically lose chemotaxis up spatial Ca2+ gradients. The generic chemotaxis term is imprecise; the specific Ca2+-gradient role is captured by the cell-motility-in-response-to-calcium term.
Reason: IplA is not required for chemotaxis generally (cAMP chemotaxis is normal); its role is restricted to Ca2+-gradient chemotaxis, so the broad term is a non-core, over-general description.
Supporting Evidence:
PMID:22375061
cells lose the capacity to undergo chemotaxis in response to a spatial gradient
|
|
GO:0071260
cellular response to mechanical stimulus
|
IMP
PMID:35859163 Calcium responses to external mechanical stimuli in the mult... |
KEEP AS NON CORE |
Summary: IplA contributes to Ca2+ bursts triggered by mechanical stimulation of slugs, one of two pathways (ER release via IplA plus extracellular influx) mediating mechanosensory Ca2+ signaling.
Reason: Supported by reduced mechanically induced Ca2+ bursts in iplA-null slugs; a downstream physiological role of the channel rather than its core molecular function.
Supporting Evidence:
PMID:35859163
response to mechanical stimuli are partially mediated by
PMID:35859163
the calcium channel, IplA, the homolog of the IP3 receptor, is essential for its elevation
|
|
GO:0140986
G protein-coupled chemorepellent receptor signaling pathway
|
IMP
PMID:30462573 An endogenous chemorepellent directs cell movement by inhibi... |
KEEP AS NON CORE |
Summary: iplA-null cells fail to move away from the chemorepellent AprA, implicating IplA in the AprA chemorepulsion signaling pathway.
Reason: Supported by the AprA chemorepulsion phenotype of iplA-null cells; a downstream Ca2+-dependent process rather than the core channel function.
Supporting Evidence:
PMID:30462573
iplA− cells did not move away from AprA
PMID:30462573
IplA and PkcA, although not necessary for chemoattraction toward cAMP, are necessary for chemorepulsion from AprA
|
|
GO:0016020
membrane
|
ISS
PMID:10970875 Ca(2+) signalling is not required for chemotaxis in Dictyost... |
KEEP AS NON CORE |
Summary: Sequence-based (ISS) membrane localization from the predicted multi-pass transmembrane topology. Correct but generic; the ER membrane term is the informative one.
Reason: Membrane is a high-level, uninformative location; IplA is more precisely an ER membrane multi-pass channel.
Supporting Evidence:
PMID:10970875
it is the membrane channel of an intracellular Ca 2+ store
|
|
GO:1903665
negative regulation of asexual reproduction
|
IMP
PMID:34154396 An Autocrine Negative Feedback Loop Inhibits Dictyostelium d... |
KEEP AS NON CORE |
Summary: IplA is required for polyphosphate-induced inhibition of proliferation, acting within an autocrine IP3/Ca2+ negative-feedback loop that limits cell density.
Reason: Supported by reduced polyphosphate sensitivity and loss of the polyphosphate-triggered cytosolic Ca2+ rise in iplA-null cells; a downstream Ca2+-signaling role rather than the core molecular function.
Supporting Evidence:
PMID:34154396
inositol 1,4,5-trisphosphate (IP3) receptor-like protein A (IplA), polyphosphate
PMID:34154396
Polyphosphate also upregulates cytosolic Ca2+, and this requires GrlD
|
|
GO:0032060
bleb assembly
|
IMP
PMID:26317626 Microtubule-Mediated Inositol Lipid Signaling Plays Critical... |
KEEP AS NON CORE |
Summary: iplA-null cells extend blebs more frequently than wild type, implicating IplA (Ca2+ channel) in the regulation of blebbing.
Reason: Supported by the increased blebbing phenotype of iplA-null cells; a downstream role in membrane dynamics rather than the core channel function.
Supporting Evidence:
PMID:26317626
extended blebs more frequently than wild type cells
|
|
GO:0031152
aggregation involved in sorocarp development
|
IMP
PMID:22375061 The IplA Ca2+ channel of Dictyostelium discoideum is necessa... |
KEEP AS NON CORE |
Summary: IplA has a fundamental role in natural aggregation, since iplA-null cells lose the ability to reorient toward the aggregation center at the onset of each natural cAMP wave.
Reason: Supported by the natural-aggregation defect of iplA-null cells; a developmental consequence of impaired Ca2+ signaling rather than the core molecular function.
Supporting Evidence:
PMID:22375061
has a fundamental role in natural aggregation
|
|
GO:0097231
cell motility in response to calcium ion
|
IMP
PMID:22375061 The IplA Ca2+ channel of Dictyostelium discoideum is necessa... |
ACCEPT |
Summary: IplA is essential for chemotaxis in a spatial gradient of Ca2+ while dispensable for cAMP chemotaxis, making it the signature Ca2+-gradient motility component in Dictyostelium.
Reason: This is the most specific and distinctive experimentally supported process for iplA, directly reflecting the loss of Ca2+-gradient chemotaxis in null cells.
Supporting Evidence:
PMID:22375061
mutant of the putative IplA Ca(2+) channel gene, iplA(-), undergoes normal
PMID:22375061
cells lose the capacity to undergo chemotaxis in response to a spatial gradient
|
|
GO:0005509
calcium ion binding
|
IMP
PMID:22375061 The IplA Ca2+ channel of Dictyostelium discoideum is necessa... |
MARK AS OVER ANNOTATED |
Summary: Calcium ion binding inferred from the Ca2+-chemotaxis phenotype. As a generic sensor-type binding term it does not capture IplA's function; the informative molecular function is (intracellular) calcium channel activity.
Reason: IplA conducts Ca2+ through a channel; annotating generic calcium ion binding (typically an EF-hand sensor function) over-annotates the protein. The channel-activity terms represent the true molecular function.
Supporting Evidence:
PMID:10970875
InsP 3 /RyR receptor family of ligand-gated Ca 2+ channels
|
|
GO:0005886
plasma membrane
|
IDA
PMID:22375061 The IplA Ca2+ channel of Dictyostelium discoideum is necessa... |
KEEP AS NON CORE |
Summary: A minor plasma-membrane pool is consistent with IP3R-family behavior (these channels are found at low levels in the plasma membrane), but the primary location of IplA is the ER membrane and whether it acts as a plasma-membrane channel remains uncertain.
Reason: The curator annotation is retained, but plasma membrane is a minor/uncertain location relative to the ER membrane; mechanistically IplA is considered more likely the channel of an intracellular Ca2+ store.
Supporting Evidence:
PMID:22375061
usually located in the membrane of endoplasmic reticulum and vesicles, but are also found at low levels in the plasma membrane
PMID:10970875
it is the membrane channel of an intracellular Ca 2+ store
|
|
GO:0030659
cytoplasmic vesicle membrane
|
IDA
PMID:22375061 The IplA Ca2+ channel of Dictyostelium discoideum is necessa... |
KEEP AS NON CORE |
Summary: A vesicle-membrane pool is plausible for an IP3R-family channel, though the ER membrane is the principal location.
Reason: Retained as a secondary location; the core, best-supported localization is the endoplasmic reticulum membrane.
Supporting Evidence:
PMID:22375061
usually located in the membrane of endoplasmic reticulum and vesicles, but are also found at low levels in the plasma membrane
|
|
GO:0034670
chemotaxis to arachidonate
|
IMP
PMID:18202452 Arachidonic acid is a chemoattractant for Dictyostelium disc... |
KEEP AS NON CORE |
Summary: Arachidonic acid is a chemoattractant whose Ca2+-dependence differs between wild type and the iplA-null HM1049 strain, implicating IplA in the Ca2+-dependent arm of arachidonate chemotaxis.
Reason: Supported by the altered EGTA sensitivity of arachidonate chemotaxis in iplA-null cells; a downstream Ca2+-dependent process rather than the core channel function.
Supporting Evidence:
PMID:18202452
iplA gene encoding a putative Ins(1,4,5)P3 -receptor had been knocked out
PMID:18202452
chemotaxis was only slightly affected by EGTA
|
|
GO:0051209
release of sequestered calcium ion into cytosol
|
IMP
PMID:18359017 Mechano-chemical signaling maintains the rapid movement of D... |
ACCEPT |
Summary: As the ER IP3R-family channel, IplA governs Ca2+ efflux from ER stores into the cytosol and contributes to the intracellular-source Ca2+ transients seen during mechanochemical signaling.
Reason: Release of sequestered Ca2+ into the cytosol is the direct physiological readout of IplA channel activity and is well supported across the literature.
Supporting Evidence:
PMID:18077554
a ligand-gated channel governing Ca(2+) efflux from endoplasmic reticulum stores
PMID:18359017
small, brief, Ca2+ transients in randomly moving wild-type
|
|
GO:0030244
cellulose biosynthetic process
|
IMP
PMID:18077554 The inositol 1,4,5-trisphosphate receptor is required to sig... |
KEEP AS NON CORE |
Summary: The iplA-null mutation prevents DIF-induced cellulose shell synthesis around dying cells, consistent with IP3R/Ca2+ control of genes governing cellulose synthesis.
Reason: Supported by the loss of cellulose shell synthesis in iplA-null cells under DIF; an indirect downstream, transcriptionally mediated consequence of Ca2+ signaling rather than a core molecular function.
Supporting Evidence:
PMID:18077554
The iplA − mutation prevented cellulose shell synthesis around cells subjected to DIF
|
|
GO:0048102
autophagic cell death
|
IMP
PMID:18077554 The inositol 1,4,5-trisphosphate receptor is required to sig... |
KEEP AS NON CORE |
Summary: Inactivation of iplA, the only IP3R gene in Dictyostelium, prevents DIF-induced autophagic cell death, defining an IplA/IP3R-dependent Ca2+ pathway for ACD.
Reason: Strongly supported by the ACD-resistant phenotype of iplA-null cells; a downstream Ca2+-dependent developmental process rather than the core channel function.
Supporting Evidence:
PMID:18077554
inactivation of the iplA gene, the only gene encoding an inositol
PMID:18077554
a ligand-gated channel governing Ca(2+) efflux from endoplasmic reticulum stores
|
|
GO:0006816
calcium ion transport
|
IMP
PMID:17077123 Influx of extracellular Ca2+ is necessary for electrotaxis i... |
ACCEPT |
Summary: IplA is described as the gene responsible for chemoattractant-induced cytosolic Ca2+ increase. Notably, this same study shows iplA is NOT required for electrotaxis-associated Ca2+ influx, underscoring that IplA mediates a specific (chemoattractant-linked) calcium transport route.
Reason: Calcium ion transport is supported by IplA's established role in the chemoattractant-induced cytosolic Ca2+ increase; note that this paper also shows the electrotaxis Ca2+ rise is iplA-independent, so the transport role is chemoattractant-specific.
Supporting Evidence:
PMID:17077123
Different roles of the iplA gene in chemoattractant-induced
|
|
GO:0006816
calcium ion transport
|
IMP
PMID:10970875 Ca(2+) signalling is not required for chemotaxis in Dictyost... |
ACCEPT |
Summary: Disruption of iplA abolishes chemoattractant-stimulated Ca2+ entry and the cytosolic Ca2+ rise, directly demonstrating a role in calcium ion transport.
Reason: Strong experimental (IMP) support for calcium ion transport from the original characterization of the iplA-null mutant.
Supporting Evidence:
PMID:10970875
Ca(2+) entry in response to chemoattractants is abolished
|
|
GO:0015085
calcium ion transmembrane transporter activity
|
ISS
PMID:10970875 Ca(2+) signalling is not required for chemotaxis in Dictyost... |
ACCEPT |
Summary: Sequence homology places IplA in the InsP3R/RyR family of ligand-gated Ca2+ channels, and the null phenotype supports Ca2+ transmembrane transporter activity.
Reason: A core molecular-function annotation consistent with the channel/transporter role; supported by both sequence family placement and the loss of Ca2+ fluxes in null cells.
Supporting Evidence:
PMID:10970875
InsP 3 /RyR receptor family of ligand-gated Ca 2+ channels
|
IplA is an inositol 1,4,5-trisphosphate (IP3)-gated intracellular calcium-release channel
(focus type: function_assignment; slug:ipla-ip3-gated-channel)
Verdict: PARTIALLY SUPPORTED — with the specific "IP3-gated" molecular function classified as INFERENCE-ONLY / OVER-ANNOTATED relative to direct evidence.
The hypothesis splits cleanly into two claims that carry very different levels of support:
"IplA is an intracellular calcium-release channel of the IP3R/RyR superfamily." This is well supported. IplA (Q9NA13) is a 3,177-residue protein that is the single-copy structural ortholog of the inositol-1,4,5-trisphosphate receptor / ryanodine receptor (IP3R/RyR) channel superfamily in Dictyostelium. It carries the diagnostic RIH domain, the armadillo-type "IP3 receptor binding core, domain 2" fold, and a 6-transmembrane pore-forming C-terminus. It is genetically required for agonist-evoked and Ca²⁺-gradient-evoked cytosolic Ca²⁺ signalling. A channel/transporter identity is justified.
"…that is IP3-gated" — i.e., that the protein directly binds IP3 and that IP3 binding opens its conductance. This is NOT directly supported. The GO terms encoding this claim (GO:0005220 IP3-gated calcium channel activity; GO:0070679 IP3 binding) exist in UniProt only as electronic family inference (IEA:InterPro). No primary study has ever demonstrated IP3 binding by IplA or IP3-gated conductance. Computational mapping of the canonical IP3-coordinating residues onto IplA failed (0 of 9 residues confidently mapped; the metazoan MIR domain is absent). Multiple Ca²⁺-release pathways in Dictyostelium are demonstrably iplA-independent, and the primary literature consistently hedges — calling it a "putative" IP3 receptor and offering a competing interpretation of IplA as a Ca²⁺-sensing receptor rather than an IP3-gated effector.
Bottom line for the curator: Retain the IP3R-family channel identity and the genetically-supported role in intracellular Ca²⁺ release, but flag the "IP3-gated" molecular function as inferred/unverified. The most defensible molecular-function annotation is a generalized calcium transmembrane transporter / channel term rather than the specific IP3-gated calcium channel activity term, unless and until direct IP3-binding or IP3-gating data are produced. This is a lead requiring curator verification.
IplA is annotated in UniProt (Q9NA13) as a 3,177-amino-acid "Inositol 1,4,5-trisphosphate receptor-like protein A," with the family-level SIMILARITY statement "Belongs to the InsP3 receptor family." Its domain architecture is unambiguously that of the IP3R/RyR intracellular Ca²⁺-release channel superfamily:
| Signature | Description |
|---|---|
| IPR000493 | InsP3 receptor (InsP3_rcpt) |
| IPR000699 / PF01365 | RIH domain (RyR and IP3R Homology) |
| IPR013662 / PF08454 | RIH-associated domain |
| IPR015925 | Ryanodine receptor / IP3 receptor |
| IPR035910 + SSF100909 | "IP3 receptor type 1 binding core, domain 2" (armadillo-type fold; 2 SUPFAM matches) |
| PF01365 (RYDR_ITPR ×2) | Ryanodine/IP3 receptor channel region |
| PANTHER PTHR13715:SF99 | IP3R/RyR family |
| PRINTS PR00779 | INSP3RECEPTR |
The topology matches the canonical channel fold: a large N-terminal cytoplasmic region (~residues 1–1175) followed by 6 transmembrane helices (~1176–3016) forming a pore-like C-terminus. Lam & Golstein (2008) describe iplA as "the only gene encoding an inositol 1,4,5-trisphosphate receptor (IP3R) in this organism" (PMID: 18077554). Dictyostelium thus has a single-copy member of this family, which removes any concern about paralog confusion at the level of gene identity — there is exactly one IP3R-family gene, and IplA is it.
This finding supports the channel/transporter half of the hypothesis. The evolutionary and structural signal that IplA belongs to the IP3R/RyR fold is strong and internally consistent across InterPro, Pfam, SUPFAM, PANTHER, and PRINTS.
The genetic case for IplA in Ca²⁺ signalling is real but bounded:
Critically, the GO annotations that encode the specific mechanistic claim — GO:0005220 (IP3-gated calcium channel activity) and GO:0070679 (IP3 binding) — are present in UniProt only as IEA:InterPro (electronic family inference). There is no IDA (inferred from direct assay) supporting either. Consistently, the UniProt FUNCTION field is hedged: "May be a receptor for inositol 1,4,5-trisphosphate."
This finding qualifies the hypothesis. IplA is genetically necessary for a subset of Ca²⁺ responses, but "necessary for agonist-evoked Ca²⁺ entry" is not the same as "IP3-gated Ca²⁺-release channel." The observation that CICR and capacitative entry proceed normally without IplA shows that much of the cell's Ca²⁺-release machinery does not route through IplA.
A direct interrogation of the sequence was performed (provenance file: ipla_ip3_residue_alignment.txt). The InterPro API returns 14 signatures for Q9NA13 confirming the channel/RIH binding-core fold, but the MIR domain (PF02815 / IPR016093) — a hallmark of the N-terminal IP3-binding/suppressor apparatus of metazoan IP3R and RyR — is not matched.
A custom Smith–Waterman alignment (BLOSUM62) of IplA residues 1–1300 against the human ITPR1 (P29994) N-terminus produced only one extendable local alignment, covering the suppressor-domain region (human ~81–246 vs IplA ~128–279) at just 28.7% identity. Forcing an alignment across the IP3-binding core (human 224–604) yielded only a short 22-residue segment (45% over 22 aa) that did not extend. As a result, 0 of the 9 canonical IP3-coordinating residues of human ITPR1 (R265, T266, R269, R504, K508, R511, Y567, R568, K569) could be confidently mapped onto IplA.
This finding is the strongest computational argument against the specific "IP3-gated" molecular function. The overall channel fold is conserved, but the ligand-recognition apparatus that defines IP3 gating in metazoans is not recognizably present. This is consistent with an ancient, divergent family member that retained the pore/channel architecture while its N-terminal ligand-sensing module diverged beyond recognition — leaving open whether IplA is gated by IP3 at all.
A comprehensive NCBI eutils search of "iplA Dictyostelium" (15 records) found no primary study demonstrating direct IP3 binding or IP3-gated conductance. The recurring language and findings across the literature undercut a definitive IP3-gated assignment:
This finding reinforces the "inference-only" status of the IP3-gated claim and identifies a credible competing hypothesis (Ca²⁺-sensing receptor) that the current evidence cannot exclude.
The evidence resolves into a two-layer model in which the identity claim is solid and the gating mechanism claim is unproven:
HYPOTHESIS: "IP3-gated intracellular Ca2+-release channel"
+----------------------------+-----------------------------+
| LAYER 1: CHANNEL IDENTITY | LAYER 2: GATING MECHANISM |
| (SUPPORTED) | (INFERENCE-ONLY) |
+----------------------------+-----------------------------+
Sequence/domain | RIH domain [OK] | MIR domain ABSENT [NO] |
| IP3R binding-core fold[OK] | 0/9 IP3-contact residues |
| 6-TM pore [OK] | mappable [NO] |
| single-copy IP3R ortholog | |
+----------------------------+-----------------------------+
Genetics | iplA- abolishes agonist- | Direct IP3 binding: |
| evoked Ca2+ entry [OK] | NEVER assayed [NO] |
| required for DIF autophagic | IP3-gated conductance: |
| cell death [OK] | NEVER measured [NO] |
+----------------------------+-----------------------------+
Counter-evidence | | CICR intact in iplA- |
| | Capacitative entry intact |
| | P2X purinergic influx intact|
| | Competing "Ca2+-sensor"model|
+----------------------------+-----------------------------+
GO:0005220 / GO:0070679 = IEA:InterPro ONLY (no IDA)
The most parsimonious reading is: IplA is a genuine IP3R/RyR-fold intracellular Ca²⁺ channel that is genetically required for a specific branch of agonist-evoked Ca²⁺ signalling, but whether IP3 is its physiological gating ligand is untested and computationally doubtful. The absence of the MIR domain and the non-mappability of IP3-contact residues suggest the ligand-sensing module has diverged substantially from the metazoan template. The "IP3-gated" label is a homology-based family inference propagated by InterPro, not a measured property of the Dictyostelium protein.
An important nuance from the pathway literature: Dictyostelium IP3/Ca²⁺ signalling does operate upstream of IplA in some contexts (e.g., polyphosphate → PLC → IP3 → cytosolic Ca²⁺ inhibits proliferation, and IplA is one of several components required — PMID: 34154396). But "IplA acts in a pathway where IP3 is produced" is not evidence that "IplA is the IP3 receptor that IP3 gates." IplA could act downstream of, parallel to, or independent of the IP3 sensing step within these pathways.
| Citation (PMID) | Evidence type | Supports / Refutes / Qualifies / Competing | Claim tested | Key finding | Context | Confidence & limitations |
|---|---|---|---|---|---|---|
| UniProt Q9NA13 + InterPro | Structural / evolutionary; database | Supports (identity); Qualifies (gating) | IplA belongs to IP3R/RyR channel family | RIH domain, IP3R binding-core fold, 6-TM pore; GO:0005220/GO:0070679 are IEA:InterPro only | Sequence/domain | High for family identity; the MF gating terms are electronic inference, not IDA |
| PMID: 18077554 (Lam & Golstein 2008) | Mutant phenotype; review-level statement | Supports (identity) | Single IP3R-family gene; role in cell death | "the only gene encoding an inositol 1,4,5-trisphosphate receptor (IP3R) in this organism"; iplA needed for DIF-induced autophagic cell death | Dictyostelium | High for single-copy identity; "IP3R" here is a family label, not a gating assay |
| PMID: 10970875 (Traynor et al. 2000) | Mutant phenotype | Supports (channel role); Qualifies (gating) | iplA required for agonist-evoked Ca²⁺ entry | iplA-null abolishes chemoattractant-evoked Ca²⁺ entry; resting [Ca²⁺] normal; chemotaxis unaffected | Dictyostelium aggregation | High for genetic requirement; does not test IP3 binding or gating |
| PMID: 15760480 (Schaloske et al. 2005) | Mutant phenotype | Qualifies / partly refutes | Which Ca²⁺ pathways need IplA | Capacitative entry fully operative in iplA⁻; store release still occurs; sensitivity shifted ~100× | Dictyostelium | High; shows multiple Ca²⁺ routes are IplA-independent |
| PMID: 17854889 (Malchow et al. 2008) | Mutant phenotype | Qualifies / refutes (for CICR) | Is CICR IplA-dependent? | CICR "virtually unchanged" in iplA⁻; calls IplA "putative IP3 or ryanodine receptor" | Dictyostelium | High; a major Ca²⁺-release mechanism does not require IplA |
| PMID: 22375061 (Lusche et al. 2012) | Mutant phenotype; competing model | Competing | Is IplA an IP3 effector or a Ca²⁺ sensor? | "putative IplA Ca²⁺ channel"; IplA "either the Ca²⁺ chemotaxis receptor or an essential component of the Ca²⁺ chemotaxis regulatory pathway" | Dictyostelium chemotaxis | High; explicitly offers a Ca²⁺-sensing alternative |
| PMID: 18486207 (Ludlow et al. 2008) | Mutant phenotype | Qualifies | Is purinergic Ca²⁺ influx IplA-dependent? | P2X ATP/ADP-evoked Ca²⁺ influx "not affected by deletion of… iplA" | Dictyostelium | High; another IplA-independent Ca²⁺ pathway |
| PMID: 40295210 (Kim et al. 2025) | Mutant phenotype | Qualifies / competing | IplA role in external-Ca²⁺ responses | Fewer iplA⁻ cells respond to external Ca²⁺; IplA "modulat[es] timing and amplitude"; acidic stores contribute | Dictyostelium | Moderate–high; frames IplA as modulator/sensor |
| PMID: 34154396 (autocrine feedback 2021) | Mutant phenotype; pathway | Qualifies | IplA in IP3/Ca²⁺ proliferation-inhibition pathway | iplA⁻ cells have reduced polyphosphate sensitivity; polyphosphate upregulates IP3 and cytosolic Ca²⁺ | Dictyostelium | Moderate; pathway context, not a direct gating assay |
Custom Smith–Waterman alignment (this study; ipla_ip3_residue_alignment.txt) |
Computational | Refutes (gating specificity) | Are IP3-contact residues conserved in IplA? | 0/9 canonical human ITPR1 IP3-coordinating residues mappable; MIR domain absent; best N-terminal identity 28.7% | In silico vs human ITPR1 P29994 | Moderate; local-alignment limitation, no experimental structure of IplA |
Lead requiring curator verification. The current UniProt annotations relevant to this hypothesis are:
| GO term | Aspect | Current evidence code | Recommended action (lead) |
|---|---|---|---|
| GO:0005220 — inositol 1,4,5-trisphosphate-gated calcium channel activity | MF | IEA:InterPro | Do not promote to experimental. Flag as inferred-only; consider generalizing to GO:0005262 (calcium channel activity) or GO:0015085 (calcium ion transmembrane transporter activity), which the phenotype data support without asserting the unproven IP3-gating mechanism. |
| GO:0070679 — inositol 1,4,5-trisphosphate binding | MF | IEA:InterPro | Do not promote. No direct binding assay exists; the ligand-binding residues are not computationally supported. Retain only as electronic inference or remove if the curator requires experimental backing for MF binding claims. |
| Intracellular Ca²⁺ release / calcium-mediated signalling | BP | Phenotype-supported | Retain/support. Genetic requirement for agonist-evoked Ca²⁺ entry (Traynor 2000) and DIF-induced autophagic cell death (Lam 2008) justify a BP annotation for Ca²⁺-mediated signalling. |
| Endoplasmic reticulum / intracellular membrane (CC) | CC | Homology/inference | Retain as inferred, consistent with an ER-localized IP3R/RyR-fold channel; note that direct localization data in Dictyostelium are limited. |
Guidance mapping to the focus type (function_assignment): the gene product directly has the broad channel/transporter function (well supported), but does not have demonstrated evidence for the specific IP3-gated activity or IP3 binding. The specific MF terms are therefore too strong for anything above IEA and should be retained only as electronic inference or generalized. Avoid defaulting to "protein binding" — the informative, defensible MF is a calcium channel / calcium transmembrane transporter term.
Immediate molecular function being tested: whether the IplA polypeptide (a) binds IP3 and (b) conducts Ca²⁺ across an intracellular membrane in an IP3-dependent (gated) manner.
The curatorial danger is conflating "iplA-null abolishes Ca²⁺ entry" (a downstream, pathway-level phenotype) with "IplA is the IP3-gated channel" (a direct molecular mechanism). The data support the former, not the latter.
Competing "Ca²⁺-sensing receptor" model. Lusche et al. 2012 (PMID: 22375061) explicitly propose IplA as the Ca²⁺ chemotaxis receptor or an essential component of Ca²⁺-sensing — a role in which Ca²⁺ (not IP3) is the relevant ligand/signal. Kim et al. 2025 (PMID: 40295210) similarly frame IplA as a modulator of responses to external Ca²⁺.
IplA-independent Ca²⁺ pathways. Capacitative/store-operated entry (Schaloske 2005), CICR (Malchow 2008), and P2X purinergic influx (Ludlow 2008) all proceed without IplA. If IplA were the dominant IP3-gated ER Ca²⁺-release channel, one would expect broader disruption of store release; instead, store release is largely preserved.
Divergent ligand-sensing module. The absence of the MIR domain and non-conservation of IP3-contact residues raise the possibility that the Dictyostelium protein is gated by a different ligand or mechanism than metazoan IP3Rs. The family label "IP3 receptor-like" (note the "-like") reflects this uncertainty.
Database carry-over / frequency bias. The IP3-gated MF terms derive from InterPro family inference. Because the family is named after the metazoan IP3 receptor, the specific gating annotation propagates automatically to all members — a classic over-annotation risk when the defining ligand-binding residues are not verified in the target.
No paralog confusion at the gene level. There is only one IP3R-family gene in Dictyostelium, so the ambiguity is not "which paralog" but "does this single ortholog retain the ancestral IP3-gating mechanism."
| Gap | What was checked | Why it matters for curation | What would resolve it |
|---|---|---|---|
| No direct IP3-binding data | UniProt evidence codes; 15-record eutils literature sweep | GO:0070679 (IP3 binding) rests entirely on electronic inference | Radioligand or fluorescence-polarization IP3-binding assay on recombinant IplA N-terminus |
| No IP3-gated conductance data | Literature sweep; no electrophysiology found | GO:0005220 (IP3-gated channel) unproven at the protein level | Single-channel recording / Ca²⁺-flux assay of IplA reconstituted in bilayers or ER vesicles ± IP3 |
| IP3-contact residues not mappable | Custom Smith–Waterman vs human ITPR1; InterPro domain scan | Sequence divergence undermines the specific gating claim | Experimental or high-confidence predicted 3D structure of the IplA ligand-binding core; docking of IP3 |
| MIR domain absent | InterPro/Pfam scan (PF02815 not matched) | The metazoan IP3-sensing apparatus may not be present | Structural/biochemical characterization of the IplA N-terminus |
| Subcellular localization in Dictyostelium | Homology inference only | CC annotation (ER) is inferred, not directly shown | GFP-IplA localization / immuno-EM in Dictyostelium |
| Whether Ca²⁺ vs IP3 is the physiological gating signal | Competing-model literature (Lusche, Kim) | Determines correct MF term (IP3-gated vs Ca²⁺-sensing/CICR) | Structure–function assays testing gating by IP3 vs Ca²⁺ |
To distinguish "IP3-gated channel" from "Ca²⁺-sensing receptor" or "non-IP3 channel," the following are prioritized by decisiveness and feasibility:
Direct IP3-binding assay (highest priority): express the IplA N-terminal cytoplasmic region (residues ~1–1175) and test IP3 binding by radioligand ([³H]-IP3) competition or isothermal titration calorimetry. A negative result would strongly refute the IP3-gated claim; a positive result would convert GO:0070679 from IEA to IDA.
IP3-gated conductance assay: reconstitute full-length IplA into planar lipid bilayers or ER-derived vesicles and measure Ca²⁺ flux/single-channel activity in response to IP3 (and, as controls, Ca²⁺ and cADPR/NAADP). This directly tests GO:0005220.
Structure-guided residue analysis: obtain an experimental or AlphaFold structure of the IplA binding core, dock IP3, and test predicted contact residues by mutagenesis coupled to functional Ca²⁺ readout in iplA⁻ rescue.
Rescue specificity: complement iplA⁻ cells with wild-type IplA vs a putative binding-pocket mutant and ask whether agonist-evoked Ca²⁺ entry and DIF-induced cell death are restored only by the IP3-competent form.
Comparative pathway epistasis: manipulate PLC/IP3 levels (e.g., PLC-null, or acute IP3 uncaging) and measure IplA-dependent Ca²⁺ responses to test whether IP3 is upstream of IplA function specifically (vs merely present in the same pathway).
Localization: GFP-tagged IplA in Dictyostelium to confirm ER vs acidic-store vs plasma-membrane localization (relevant to the Ludlow/Kim acidic-store observations).
ipla_ip3_residue_alignment.txt — custom Smith–Waterman (BLOSUM62) alignment of IplA (1–1300) vs human ITPR1 (P29994), including the attempted mapping of the 9 canonical IP3-coordinating residues (0/9 confidently mapped) and the InterPro/Pfam domain scan showing the MIR domain absent. This is the computed basis for Finding 3.Prepared for AI Gene Review hypothesis-level curation. All experimental claims are attributed to the cited primary literature; all sequence/domain analyses are reported conservatively and distinguish direct results from homology inference.
id: Q9NA13
gene_symbol: iplA
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:44689
label: Dictyostelium discoideum
description: IplA is the sole inositol 1,4,5-trisphosphate/ryanodine receptor family
member in Dictyostelium discoideum and the only recognizable homolog of the metazoan
IP3 receptor in this organism. It is a very large (3177 aa) multi-pass endoplasmic
reticulum membrane protein with a long cytoplasmic N-terminal region containing predicted
InsP3-binding residues and a C-terminal six-transmembrane channel domain, and it assembles
into the intracellular ligand-gated calcium-release channel that governs Ca2+ efflux
from ER stores into the cytosol. Genetic ablation of iplA abolishes the chemoattractant
(cAMP/folate)-stimulated Ca2+ entry and the accompanying rise in free cytosolic Ca2+,
while leaving resting cytosolic Ca2+, cAMP chemotaxis, cGMP production and MAP kinase
signaling intact. IplA is specifically required for chemotaxis up spatial Ca2+ gradients
and contributes to a wide range of Ca2+-dependent processes, including natural aggregation,
arachidonate chemotaxis, AprA-mediated chemorepulsion, mechanosensory Ca2+ bursts in
slugs, regulation of blebbing, DIF-induced autophagic cell death with cellulose shell
synthesis, and polyphosphate/IP3-Ca2+ feedback inhibition of proliferation. Although
it is clearly a Ca2+ channel of the InsP3R/RyR family, direct biochemical demonstration
that IplA is gated by InsP3 is still lacking.
existing_annotations:
- term:
id: GO:0030659
label: cytoplasmic vesicle membrane
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: Phylogenetic (IBA) inference placing IplA in vesicle membranes. IP3-receptor
family channels reside chiefly in the ER membrane but are also found in vesicle
membranes, so this is plausible but not the principal, best-supported location.
action: KEEP_AS_NON_CORE
reason: The endoplasmic reticulum membrane is the established primary location for
IplA; a cytoplasmic vesicle membrane pool is plausible for an IP3R-family channel
but is secondary to the core ER-membrane localization.
supported_by:
- reference_id: PMID:22375061
supporting_text: usually located in the membrane of endoplasmic reticulum and vesicles,
but are also found at low levels in the plasma membrane
- term:
id: GO:0005220
label: inositol 1,4,5-trisphosphate-gated calcium channel activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: InterPro2GO transfer of the specific mammalian ITPR molecular function.
IplA is the sole IP3R-family homolog and functions as an intracellular Ca2+-release
channel, but direct biochemical evidence that it is gated by InsP3 is explicitly
lacking, so the specific InsP3-gated term over-reaches what has been demonstrated.
action: MODIFY
reason: The demonstrated activity is that of an (intracellular) calcium channel;
InsP3-gating is inferred from sequence homology and conserved binding residues
but has not been shown biochemically. Generalizing the overly specific InsP3-gated
term to calcium channel activity better matches the evidence.
proposed_replacement_terms:
- id: GO:0005262
label: calcium channel activity
supported_by:
- reference_id: PMID:10970875
supporting_text: biochemical evidence that IplA is an InsP 3 receptor is still lacking
- reference_id: PMID:40295210
supporting_text: IplA, a Dictyostelium protein analogous to the mammalian IP3 receptor,
is a ligand-gated calcium channel responsible for calcium release from the endoplasmic
reticulum
- term:
id: GO:0005262
label: calcium channel activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: IplA is an intracellular ligand-gated calcium-release channel; ablation
of iplA abolishes chemoattractant-stimulated Ca2+ fluxes. This is the core molecular
function of the gene product.
action: ACCEPT
reason: Calcium channel activity is the well-supported core function, consistent
with the InsP3R/RyR family assignment and the loss of Ca2+ fluxes in iplA-null cells.
supported_by:
- reference_id: PMID:10970875
supporting_text: InsP 3 /RyR receptor family of ligand-gated Ca 2+ channels
- reference_id: PMID:40295210
supporting_text: IplA, a Dictyostelium protein analogous to the mammalian IP3 receptor,
is a ligand-gated calcium channel responsible for calcium release from the endoplasmic
reticulum
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000117
qualifier: located_in
review:
summary: Generic ARBA-derived cytoplasm localization. Not incorrect (the cytoplasmic
N-terminal region is large) but uninformative relative to the specific ER-membrane
localization.
action: KEEP_AS_NON_CORE
reason: Cytoplasm is a high-level, uninformative location for a multi-pass ER membrane
channel; the endoplasmic reticulum membrane term captures the biology better.
- term:
id: GO:0005783
label: endoplasmic reticulum
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: located_in
review:
summary: The endoplasmic reticulum is the established compartment for IplA, consistent
with its role as an ER Ca2+-store release channel.
action: ACCEPT
reason: ER localization is supported by the UniProt subcellular location and by the
protein's function in releasing Ca2+ from ER stores.
supported_by:
- reference_id: PMID:18077554
supporting_text: a ligand-gated channel governing Ca(2+) efflux from endoplasmic
reticulum stores
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: The most precise and best-supported location for IplA, a multi-pass ER membrane
channel that releases Ca2+ from ER stores into the cytosol.
action: ACCEPT
reason: ER membrane localization matches the UniProt subcellular location, the six-transmembrane
topology, and the ER Ca2+-store release function.
supported_by:
- reference_id: PMID:40295210
supporting_text: IplA, a Dictyostelium protein analogous to the mammalian IP3 receptor,
is a ligand-gated calcium channel responsible for calcium release from the endoplasmic
reticulum
- term:
id: GO:0006816
label: calcium ion transport
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: Calcium ion transport is a direct consequence of IplA channel activity and
is central to its function.
action: ACCEPT
reason: As a Ca2+ channel, IplA mediates calcium ion transport; ablation abolishes
chemoattractant-stimulated Ca2+ fluxes.
supported_by:
- reference_id: PMID:10970875
supporting_text: Ca(2+) entry in response to chemoattractants is abolished
- term:
id: GO:0016020
label: membrane
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: located_in
review:
summary: Generic membrane localization, subsumed by the more specific endoplasmic
reticulum membrane term.
action: KEEP_AS_NON_CORE
reason: Membrane is an uninformative high-level location; the ER membrane annotation
is the informative one.
- term:
id: GO:0070588
label: calcium ion transmembrane transport
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: Transmembrane movement of Ca2+ across the ER membrane is the core activity
of this channel.
action: ACCEPT
reason: IplA conducts Ca2+ across the ER membrane; this process directly reflects
its channel function.
supported_by:
- reference_id: PMID:18077554
supporting_text: a ligand-gated channel governing Ca(2+) efflux from endoplasmic
reticulum stores
- term:
id: GO:0070679
label: inositol 1,4,5 trisphosphate binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: InterPro2GO transfer based on the IP3R-family InsP3-binding domain. IplA
retains predicted InsP3-binding residues, but direct biochemical InsP3 binding
has not been demonstrated for this divergent protein.
action: KEEP_AS_NON_CORE
reason: InsP3 binding is inferred from conserved sequence features; experimental verification
is lacking (biochemical evidence that IplA is an InsP3 receptor is still lacking),
so it should not be treated as an established core function.
supported_by:
- reference_id: PMID:10970875
supporting_text: biochemical evidence that IplA is an InsP 3 receptor is still lacking
- term:
id: GO:0019722
label: calcium-mediated signaling
evidence_type: IMP
original_reference_id: PMID:40295210
qualifier: acts_upstream_of_or_within
review:
summary: iplA-null cells show a reduced proportion of cells mounting an intracellular
Ca2+ response to external calcium, placing IplA within calcium-mediated signaling.
action: ACCEPT
reason: Directly supported by the phenotype of iplA-null cells in calcium-signaling
assays; this is closely tied to the core channel function.
supported_by:
- reference_id: PMID:40295210
supporting_text: only approximately 60% of iplA-null cells were responsive to the
external calcium stimuli
- reference_id: PMID:40295210
supporting_text: IplA-related signaling pathways are involved in regulating intracellular
calcium levels in response to external calcium stimuli
- term:
id: GO:0006935
label: chemotaxis
evidence_type: IMP
original_reference_id: PMID:22375061
qualifier: acts_upstream_of_or_within
review:
summary: iplA-null cells retain normal chemotaxis to cAMP but specifically lose chemotaxis
up spatial Ca2+ gradients. The generic chemotaxis term is imprecise; the specific
Ca2+-gradient role is captured by the cell-motility-in-response-to-calcium term.
action: KEEP_AS_NON_CORE
reason: IplA is not required for chemotaxis generally (cAMP chemotaxis is normal);
its role is restricted to Ca2+-gradient chemotaxis, so the broad term is a non-core,
over-general description.
supported_by:
- reference_id: PMID:22375061
supporting_text: cells lose the capacity to undergo chemotaxis in response to a
spatial gradient
- term:
id: GO:0071260
label: cellular response to mechanical stimulus
evidence_type: IMP
original_reference_id: PMID:35859163
qualifier: acts_upstream_of_or_within
review:
summary: IplA contributes to Ca2+ bursts triggered by mechanical stimulation of slugs,
one of two pathways (ER release via IplA plus extracellular influx) mediating mechanosensory
Ca2+ signaling.
action: KEEP_AS_NON_CORE
reason: Supported by reduced mechanically induced Ca2+ bursts in iplA-null slugs;
a downstream physiological role of the channel rather than its core molecular function.
supported_by:
- reference_id: PMID:35859163
supporting_text: response to mechanical stimuli are partially mediated by
- reference_id: PMID:35859163
supporting_text: the calcium channel, IplA, the homolog of the IP3 receptor, is
essential for its elevation
- term:
id: GO:0140986
label: G protein-coupled chemorepellent receptor signaling pathway
evidence_type: IMP
original_reference_id: PMID:30462573
qualifier: acts_upstream_of_or_within
review:
summary: iplA-null cells fail to move away from the chemorepellent AprA, implicating
IplA in the AprA chemorepulsion signaling pathway.
action: KEEP_AS_NON_CORE
reason: Supported by the AprA chemorepulsion phenotype of iplA-null cells; a downstream
Ca2+-dependent process rather than the core channel function.
supported_by:
- reference_id: PMID:30462573
supporting_text: iplA− cells did not move away from AprA
- reference_id: PMID:30462573
supporting_text: IplA and PkcA, although not necessary for chemoattraction toward
cAMP, are necessary for chemorepulsion from AprA
- term:
id: GO:0016020
label: membrane
evidence_type: ISS
original_reference_id: PMID:10970875
qualifier: located_in
review:
summary: Sequence-based (ISS) membrane localization from the predicted multi-pass
transmembrane topology. Correct but generic; the ER membrane term is the informative one.
action: KEEP_AS_NON_CORE
reason: Membrane is a high-level, uninformative location; IplA is more precisely an
ER membrane multi-pass channel.
supported_by:
- reference_id: PMID:10970875
supporting_text: it is the membrane channel of an intracellular Ca 2+ store
- term:
id: GO:1903665
label: negative regulation of asexual reproduction
evidence_type: IMP
original_reference_id: PMID:34154396
qualifier: acts_upstream_of_or_within
review:
summary: IplA is required for polyphosphate-induced inhibition of proliferation, acting
within an autocrine IP3/Ca2+ negative-feedback loop that limits cell density.
action: KEEP_AS_NON_CORE
reason: Supported by reduced polyphosphate sensitivity and loss of the polyphosphate-triggered
cytosolic Ca2+ rise in iplA-null cells; a downstream Ca2+-signaling role rather
than the core molecular function.
supported_by:
- reference_id: PMID:34154396
supporting_text: inositol 1,4,5-trisphosphate (IP3) receptor-like protein A (IplA),
polyphosphate
- reference_id: PMID:34154396
supporting_text: Polyphosphate also upregulates cytosolic Ca2+, and this requires
GrlD
- term:
id: GO:0032060
label: bleb assembly
evidence_type: IMP
original_reference_id: PMID:26317626
qualifier: acts_upstream_of_or_within
review:
summary: iplA-null cells extend blebs more frequently than wild type, implicating
IplA (Ca2+ channel) in the regulation of blebbing.
action: KEEP_AS_NON_CORE
reason: Supported by the increased blebbing phenotype of iplA-null cells; a downstream
role in membrane dynamics rather than the core channel function.
supported_by:
- reference_id: PMID:26317626
supporting_text: extended blebs more frequently than wild type cells
- term:
id: GO:0031152
label: aggregation involved in sorocarp development
evidence_type: IMP
original_reference_id: PMID:22375061
qualifier: acts_upstream_of_or_within
review:
summary: IplA has a fundamental role in natural aggregation, since iplA-null cells
lose the ability to reorient toward the aggregation center at the onset of each
natural cAMP wave.
action: KEEP_AS_NON_CORE
reason: Supported by the natural-aggregation defect of iplA-null cells; a developmental
consequence of impaired Ca2+ signaling rather than the core molecular function.
supported_by:
- reference_id: PMID:22375061
supporting_text: has a fundamental role in natural aggregation
- term:
id: GO:0097231
label: cell motility in response to calcium ion
evidence_type: IMP
original_reference_id: PMID:22375061
qualifier: acts_upstream_of_or_within
review:
summary: IplA is essential for chemotaxis in a spatial gradient of Ca2+ while dispensable
for cAMP chemotaxis, making it the signature Ca2+-gradient motility component in
Dictyostelium.
action: ACCEPT
reason: This is the most specific and distinctive experimentally supported process
for iplA, directly reflecting the loss of Ca2+-gradient chemotaxis in null cells.
supported_by:
- reference_id: PMID:22375061
supporting_text: mutant of the putative IplA Ca(2+) channel gene, iplA(-), undergoes
normal
- reference_id: PMID:22375061
supporting_text: cells lose the capacity to undergo chemotaxis in response to a
spatial gradient
- term:
id: GO:0005509
label: calcium ion binding
evidence_type: IMP
original_reference_id: PMID:22375061
qualifier: enables
review:
summary: Calcium ion binding inferred from the Ca2+-chemotaxis phenotype. As a generic
sensor-type binding term it does not capture IplA's function; the informative molecular
function is (intracellular) calcium channel activity.
action: MARK_AS_OVER_ANNOTATED
reason: IplA conducts Ca2+ through a channel; annotating generic calcium ion binding
(typically an EF-hand sensor function) over-annotates the protein. The channel-activity
terms represent the true molecular function.
supported_by:
- reference_id: PMID:10970875
supporting_text: InsP 3 /RyR receptor family of ligand-gated Ca 2+ channels
- term:
id: GO:0005886
label: plasma membrane
evidence_type: IDA
original_reference_id: PMID:22375061
qualifier: located_in
review:
summary: A minor plasma-membrane pool is consistent with IP3R-family behavior (these
channels are found at low levels in the plasma membrane), but the primary location
of IplA is the ER membrane and whether it acts as a plasma-membrane channel remains
uncertain.
action: KEEP_AS_NON_CORE
reason: The curator annotation is retained, but plasma membrane is a minor/uncertain
location relative to the ER membrane; mechanistically IplA is considered more likely
the channel of an intracellular Ca2+ store.
supported_by:
- reference_id: PMID:22375061
supporting_text: usually located in the membrane of endoplasmic reticulum and vesicles,
but are also found at low levels in the plasma membrane
- reference_id: PMID:10970875
supporting_text: it is the membrane channel of an intracellular Ca 2+ store
- term:
id: GO:0030659
label: cytoplasmic vesicle membrane
evidence_type: IDA
original_reference_id: PMID:22375061
qualifier: located_in
review:
summary: A vesicle-membrane pool is plausible for an IP3R-family channel, though the
ER membrane is the principal location.
action: KEEP_AS_NON_CORE
reason: Retained as a secondary location; the core, best-supported localization is
the endoplasmic reticulum membrane.
supported_by:
- reference_id: PMID:22375061
supporting_text: usually located in the membrane of endoplasmic reticulum and vesicles,
but are also found at low levels in the plasma membrane
- term:
id: GO:0034670
label: chemotaxis to arachidonate
evidence_type: IMP
original_reference_id: PMID:18202452
qualifier: acts_upstream_of_or_within
review:
summary: Arachidonic acid is a chemoattractant whose Ca2+-dependence differs between
wild type and the iplA-null HM1049 strain, implicating IplA in the Ca2+-dependent
arm of arachidonate chemotaxis.
action: KEEP_AS_NON_CORE
reason: Supported by the altered EGTA sensitivity of arachidonate chemotaxis in iplA-null
cells; a downstream Ca2+-dependent process rather than the core channel function.
supported_by:
- reference_id: PMID:18202452
supporting_text: iplA gene encoding a putative Ins(1,4,5)P3 -receptor had been knocked
out
- reference_id: PMID:18202452
supporting_text: chemotaxis was only slightly affected by EGTA
- term:
id: GO:0051209
label: release of sequestered calcium ion into cytosol
evidence_type: IMP
original_reference_id: PMID:18359017
qualifier: acts_upstream_of_or_within
review:
summary: As the ER IP3R-family channel, IplA governs Ca2+ efflux from ER stores into
the cytosol and contributes to the intracellular-source Ca2+ transients seen during
mechanochemical signaling.
action: ACCEPT
reason: Release of sequestered Ca2+ into the cytosol is the direct physiological readout
of IplA channel activity and is well supported across the literature.
supported_by:
- reference_id: PMID:18077554
supporting_text: a ligand-gated channel governing Ca(2+) efflux from endoplasmic
reticulum stores
- reference_id: PMID:18359017
supporting_text: small, brief, Ca2+ transients in randomly moving wild-type
- term:
id: GO:0030244
label: cellulose biosynthetic process
evidence_type: IMP
original_reference_id: PMID:18077554
qualifier: acts_upstream_of_or_within
review:
summary: The iplA-null mutation prevents DIF-induced cellulose shell synthesis around
dying cells, consistent with IP3R/Ca2+ control of genes governing cellulose synthesis.
action: KEEP_AS_NON_CORE
reason: Supported by the loss of cellulose shell synthesis in iplA-null cells under
DIF; an indirect downstream, transcriptionally mediated consequence of Ca2+ signaling
rather than a core molecular function.
supported_by:
- reference_id: PMID:18077554
supporting_text: The iplA − mutation prevented cellulose shell synthesis around
cells subjected to DIF
- term:
id: GO:0048102
label: autophagic cell death
evidence_type: IMP
original_reference_id: PMID:18077554
qualifier: acts_upstream_of_or_within
review:
summary: Inactivation of iplA, the only IP3R gene in Dictyostelium, prevents DIF-induced
autophagic cell death, defining an IplA/IP3R-dependent Ca2+ pathway for ACD.
action: KEEP_AS_NON_CORE
reason: Strongly supported by the ACD-resistant phenotype of iplA-null cells; a downstream
Ca2+-dependent developmental process rather than the core channel function.
supported_by:
- reference_id: PMID:18077554
supporting_text: inactivation of the iplA gene, the only gene encoding an inositol
- reference_id: PMID:18077554
supporting_text: a ligand-gated channel governing Ca(2+) efflux from endoplasmic
reticulum stores
- term:
id: GO:0006816
label: calcium ion transport
evidence_type: IMP
original_reference_id: PMID:17077123
qualifier: acts_upstream_of_or_within
review:
summary: IplA is described as the gene responsible for chemoattractant-induced cytosolic
Ca2+ increase. Notably, this same study shows iplA is NOT required for electrotaxis-associated
Ca2+ influx, underscoring that IplA mediates a specific (chemoattractant-linked)
calcium transport route.
action: ACCEPT
reason: Calcium ion transport is supported by IplA's established role in the chemoattractant-induced
cytosolic Ca2+ increase; note that this paper also shows the electrotaxis Ca2+ rise
is iplA-independent, so the transport role is chemoattractant-specific.
supported_by:
- reference_id: PMID:17077123
supporting_text: Different roles of the iplA gene in chemoattractant-induced
- term:
id: GO:0006816
label: calcium ion transport
evidence_type: IMP
original_reference_id: PMID:10970875
qualifier: acts_upstream_of_or_within
review:
summary: Disruption of iplA abolishes chemoattractant-stimulated Ca2+ entry and the
cytosolic Ca2+ rise, directly demonstrating a role in calcium ion transport.
action: ACCEPT
reason: Strong experimental (IMP) support for calcium ion transport from the original
characterization of the iplA-null mutant.
supported_by:
- reference_id: PMID:10970875
supporting_text: Ca(2+) entry in response to chemoattractants is abolished
- term:
id: GO:0015085
label: calcium ion transmembrane transporter activity
evidence_type: ISS
original_reference_id: PMID:10970875
qualifier: enables
review:
summary: Sequence homology places IplA in the InsP3R/RyR family of ligand-gated Ca2+
channels, and the null phenotype supports Ca2+ transmembrane transporter activity.
action: ACCEPT
reason: A core molecular-function annotation consistent with the channel/transporter
role; supported by both sequence family placement and the loss of Ca2+ fluxes in
null cells.
supported_by:
- reference_id: PMID:10970875
supporting_text: InsP 3 /RyR receptor family of ligand-gated Ca 2+ channels
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: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:0000117
title: Electronic Gene Ontology annotations created by ARBA machine learning models
findings: []
- id: PMID:10970875
title: Ca(2+) signalling is not required for chemotaxis in Dictyostelium.
findings:
- statement: Disruption of iplA produces null cells in which chemoattractant-stimulated
Ca2+ entry and the cytosolic Ca2+ rise are abolished, while resting Ca2+ and cAMP
chemotaxis remain normal.
supporting_text: Ca(2+) entry in response to chemoattractants is abolished
- statement: Sequence homology places IplA in the InsP3/RyR receptor family of ligand-gated
Ca2+ channels.
supporting_text: InsP 3 /RyR receptor family of ligand-gated Ca 2+ channels
- statement: Direct biochemical evidence that IplA is an InsP3 receptor is still lacking.
supporting_text: biochemical evidence that IplA is an InsP 3 receptor is still lacking
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Original characterization of the iplA-null mutant; establishes the channel
family placement, the Ca2+-entry defect, and the caveat that InsP3 gating is unproven.
- id: PMID:17077123
title: Influx of extracellular Ca2+ is necessary for electrotaxis in Dictyostelium.
findings:
- statement: iplA is responsible for the chemoattractant-induced cytosolic Ca2+ increase,
but iplA-independent Ca2+ influx underlies electrotaxis, so iplA-null cells electrotax
normally.
supporting_text: Different roles of the iplA gene in chemoattractant-induced
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Abstract-only cache; shows iplA is required for chemoattractant-induced
Ca2+ but dispensable for electrotaxis-associated Ca2+ influx.
- id: PMID:18077554
title: The inositol 1,4,5-trisphosphate receptor is required to signal autophagic cell
death.
findings:
- statement: iplA is the only gene encoding an IP3 receptor in Dictyostelium, and its
inactivation prevents DIF-induced autophagic cell death.
supporting_text: inactivation of the iplA gene, the only gene encoding an inositol
- statement: The IP3R is a ligand-gated channel governing Ca2+ efflux from ER stores
to the cytosol.
supporting_text: a ligand-gated channel governing Ca(2+) efflux from endoplasmic reticulum
stores
- statement: The iplA mutation prevents cellulose shell synthesis around cells treated
with DIF.
supporting_text: The iplA − mutation prevented cellulose shell synthesis around cells
subjected to DIF
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Establishes the ER Ca2+-efflux channel mechanism and the ACD/cellulose
phenotypes of iplA-null cells.
- id: PMID:18202452
title: Arachidonic acid is a chemoattractant for Dictyostelium discoideum cells.
findings:
- statement: In the iplA-null HM1049 strain, arachidonate chemotaxis is only slightly
affected by EGTA, unlike wild type, implicating IplA in the Ca2+-dependent arm of
arachidonate chemotaxis.
supporting_text: chemotaxis was only slightly affected by EGTA
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Abstract-only cache; supports an iplA role in arachidonate (AA) chemotaxis
via extracellular Ca2+.
- id: PMID:18359017
title: Mechano-chemical signaling maintains the rapid movement of Dictyostelium cells.
findings:
- statement: Randomly moving cells show brief Ca2+ transients dependent on intracellular
and extracellular calcium sources during mechanochemical signaling.
supporting_text: small, brief, Ca2+ transients in randomly moving wild-type
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Abstract-only cache; UniProt attributes the intracellular-store Ca2+
burst component to IplA (with PMID:35859163).
- id: PMID:22375061
title: The IplA Ca2+ channel of Dictyostelium discoideum is necessary for chemotaxis
mediated through Ca2+, but not through cAMP, and has a fundamental role in natural
aggregation.
findings:
- statement: iplA-null cells chemotax normally in cAMP gradients but lose the capacity
to chemotax up spatial Ca2+ gradients.
supporting_text: cells lose the capacity to undergo chemotaxis in response to a spatial
gradient
- statement: IplA has a fundamental role in natural aggregation; null cells fail to
reorient toward the aggregation center at the onset of each natural cAMP wave.
supporting_text: has a fundamental role in natural aggregation
- statement: IP3 receptors are usually located in the ER and vesicle membranes and are
also found at low levels in the plasma membrane.
supporting_text: usually located in the membrane of endoplasmic reticulum and vesicles,
but are also found at low levels in the plasma membrane
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Defines the selective role of IplA in Ca2+-gradient chemotaxis and natural
aggregation; also the source of the plasma-membrane and vesicle-membrane IDA localizations.
- id: PMID:26317626
title: Microtubule-Mediated Inositol Lipid Signaling Plays Critical Roles in Regulation
of Blebbing.
findings:
- statement: iplA (Ca2+ channel)-deficient cells extend blebs more frequently than wild
type, implicating IplA in the regulation of blebbing.
supporting_text: extended blebs more frequently than wild type cells
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Supports an iplA role in bleb regulation among several Ca2+/lipid-signaling
components.
- id: PMID:30462573
title: An endogenous chemorepellent directs cell movement by inhibiting pseudopods at
one side of cells.
findings:
- statement: iplA-null cells fail to move away from the chemorepellent AprA, so IplA
is necessary for AprA chemorepulsion though not for cAMP chemoattraction.
supporting_text: IplA and PkcA, although not necessary for chemoattraction toward
cAMP, are necessary for chemorepulsion from AprA
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Supports the G protein-coupled chemorepellent (AprA) signaling annotation.
- id: PMID:34154396
title: An Autocrine Negative Feedback Loop Inhibits Dictyostelium discoideum Proliferation
through Pathways Including IP3/Ca(2).
findings:
- statement: Cells lacking IplA have reduced sensitivity to polyphosphate-induced proliferation
inhibition, and polyphosphate-induced cytosolic Ca2+ upregulation requires IplA.
supporting_text: inositol 1,4,5-trisphosphate (IP3) receptor-like protein A (IplA),
polyphosphate
- statement: Polyphosphate upregulates cytosolic Ca2+ through a pathway that requires
IplA among other components.
supporting_text: Polyphosphate also upregulates cytosolic Ca2+, and this requires
GrlD
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Supports the negative-regulation-of-proliferation (asexual reproduction)
annotation via the IP3/Ca2+ feedback loop.
- id: PMID:35859163
title: Calcium responses to external mechanical stimuli in the multicellular stage of
Dictyostelium discoideum.
findings:
- statement: IplA, the homolog of the IP3 receptor, is essential for the cAMP-induced
cytosolic Ca2+ elevation, and Ca2+ bursts induced by mechanical stimuli in slugs
are partially mediated by IplA (with an additional influx pathway).
supporting_text: the calcium channel, IplA, the homolog of the IP3 receptor, is essential
for its elevation
- statement: Mechanically induced Ca2+ bursts are partially mediated by IplA/ER release.
supporting_text: response to mechanical stimuli are partially mediated by
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Supports the cellular-response-to-mechanical-stimulus and ER Ca2+-release
roles of IplA in the multicellular (slug) stage.
- id: PMID:40295210
title: Intracellular Calcium Responses to External Calcium Stimuli in Dictyostelium.
findings:
- statement: IplA is described as a Dictyostelium ligand-gated calcium channel analogous
to the mammalian IP3 receptor, responsible for Ca2+ release from the ER.
supporting_text: IplA, a Dictyostelium protein analogous to the mammalian IP3 receptor,
is a ligand-gated calcium channel responsible for calcium release from the endoplasmic
reticulum
- statement: A significantly smaller proportion of iplA-null cells respond to external
calcium stimuli than wild type, implicating IplA in regulating intracellular calcium
responses.
supporting_text: only approximately 60% of iplA-null cells were responsive to the
external calcium stimuli
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Recent GCaMP3 imaging study; supports the calcium-mediated signaling
role of IplA and the ER Ca2+-release channel identity.
- id: file:DICDI/iplA/iplA-hypotheses/ipla-ip3-gated-channel/openscientist.md
title: OpenScientist function-assignment analysis of the IplA IP3-gated channel hypothesis
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Independent OpenScientist function-assignment run (3 iterations). Verdict
PARTIALLY SUPPORTED. The IP3R/RyR-superfamily intracellular Ca2+-release
channel identity is well supported (RIH domain, IP3-receptor-binding-core
armadillo fold, six-TM pore; single-copy in the genome, so no paralog
confusion). The specific IP3-GATED molecular function is NOT directly
supported - the metazoan MIR domain is absent, 0 of 9 canonical
IP3-coordinating residues map, no primary study demonstrates IP3 binding
or IP3-gated conductance, and the literature hedges ("putative"), with a
competing Ca2+-sensing interpretation. Directly corroborates this review's
MODIFY of GO:0005220 (IP3-gated channel) to the generic GO:0005262
(calcium channel activity). Best-supported MF is a generalized calcium
channel term pending direct IP3-binding data.
core_functions:
- description: IplA is the sole Dictyostelium homolog of the metazoan InsP3R/ryanodine
receptor family and functions as an intracellular ligand-gated calcium-release channel
in the endoplasmic reticulum membrane, conducting Ca2+ from ER stores into the cytosol.
Loss of iplA abolishes chemoattractant-stimulated Ca2+ entry and the cytosolic Ca2+
rise. InsP3 gating is inferred from homology and conserved binding residues but has
not been demonstrated biochemically.
molecular_function:
id: GO:0005262
label: calcium channel activity
directly_involved_in:
- id: GO:0051209
label: release of sequestered calcium ion into cytosol
- id: GO:0070588
label: calcium ion transmembrane transport
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
supported_by:
- reference_id: PMID:10970875
supporting_text: InsP 3 /RyR receptor family of ligand-gated Ca 2+ channels
- reference_id: PMID:10970875
supporting_text: Ca(2+) entry in response to chemoattractants is abolished
- reference_id: PMID:18077554
supporting_text: a ligand-gated channel governing Ca(2+) efflux from endoplasmic reticulum
stores
- description: Through its calcium-release channel activity, IplA is specifically required
for cell motility guided by extracellular Ca2+ gradients (Ca2+ chemotaxis), while
being dispensable for cAMP chemotaxis, and it feeds Ca2+-mediated signaling that contributes
to natural aggregation, mechanosensory responses, chemorepulsion, autophagic cell
death, and density-dependent proliferation control.
molecular_function:
id: GO:0005262
label: calcium channel activity
directly_involved_in:
- id: GO:0097231
label: cell motility in response to calcium ion
- id: GO:0019722
label: calcium-mediated signaling
supported_by:
- reference_id: PMID:22375061
supporting_text: cells lose the capacity to undergo chemotaxis in response to a spatial
gradient
- reference_id: PMID:40295210
supporting_text: IplA-related signaling pathways are involved in regulating intracellular
calcium levels in response to external calcium stimuli