Synj (synaptojanin, CG6562) is the single Drosophila synaptojanin, a 1218-residue cytosolic dual phosphoinositide phosphatase that associates peripherally with presynaptic and vesicular membranes. It has an N-terminal SAC phosphatase domain, which removes phosphate from PI(3)P, PI(4)P and PI(3,5)P2, a central inositol polyphosphate 5-phosphatase domain, which converts PI(4,5)P2 to PI(4)P, an RRM-like module and a disordered proline-rich C-terminal region that binds the SH3 domain of Endophilin. Synj is enriched at presynaptic terminals, where Endophilin recruits and stabilizes it on newly formed vesicles. There its 5-phosphatase activity removes PI(4,5)P2 to promote clathrin uncoating in synaptic vesicle endocytosis, and null mutants retain only a slowed form of classical endocytosis. Minibrain/DYRK1A phosphorylates Synj at S1029, which raises its 5-phosphatase activity and shifts retrieval between vesicle pools; calcineurin dephosphorylates this site. Its two catalytic domains act differently in bulk endocytosis. The SAC domain is needed for maturation of presynaptic autophagosomes, where it releases the PI(3)P-binding protein Atg18a. In wing imaginal discs, Synj also limits PI(4)P levels and thereby dampens Smoothened activation in Hedgehog signalling.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003676 nucleic acid binding | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO mapping from the generic RNA-binding-domain superfamily signature (IPR035979) that covers the synaptojanin RRM-like module; there is no evidence that synaptojanins bind nucleic acid. Reason: The hit is a structural superfamily match to the RRM-like fold of the synaptojanin-specific SYNJ1/2_RRM region (IPR015047, IPR034971), not a nucleic-acid-binding signature. Synaptojanin is a cytosolic membrane-lipid phosphatase, and none of the fly or ortholog studies of synaptojanin report RNA or DNA binding. Fold-level InterPro2GO transfer of nucleic acid binding is a recognized over-propagation, so this electronic row should be removed rather than left undecided. Supporting Evidence: file:DROME/Synj/Synj-uniprot.txt DR InterPro; IPR015047; SYNJ1/2_RRM. PMID:8552192 Synaptojanin has 5-phosphatase activity and its amino-terminal domain is homologous with the yeast protein Sac1 (Rsd1) |
| GO:0004439 phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Core activity of the central 5-phosphatase domain, directly assayed on fly Synj. Reason: The PAINT node PTN008514002 covers the PTHR11200 inositol 5-phosphatases, and Synj sits in subfamily SF257 with worm UNC-26 and yeast Inp52/Inp53, all experimentally characterized PI(4,5)P2 5-phosphatases. The fly product keeps the 5-phosphatase signature motifs (file:DROME/Synj/Synj-bioinformatics/RESULTS.md). Immunoprecipitated fly Synj converts BODIPY-PI(4,5)P2 to PI(4)P in vitro, and Minibrain phosphorylation at S1029 enhances this activity. A 5-phosphatase-dead transgene fails to rescue clathrin-mediated endocytosis. Supporting Evidence: PMID:24977345 increased the 5′-phosphatase activity of immunoprecipitated Synj in vitro PMID:27559170 we measured the 5′-phosphatase activity of immunoprecipitated Synj protein as assayed by conversion of BODIPY-labeled PI(4,5)P 2 to BODIPY-PI(4)P using TLC PMID:34596663 These results indicate that Synj's 5′-PPase activity, or the ability to convert PI(4,5)P2 to PI(4)P, is essential for CME file:DROME/Synj/Synj-bioinformatics/RESULTS.md human WCGDFNYR (727) aligns to fly WCGDFNYR (737), identical |
| GO:0004439 phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity | IEA GO_REF:0000003 | ACCEPT | Summary: EC 3.1.3.36 mapping to the same core 5-phosphatase activity; consistent with the IBA row and direct fly assays. Reason: The EC assignment to this entry comes from ARBA, so it is not itself evidence. The underlying claim is nonetheless correct, because fly Synj converts PI(4,5)P2 to PI(4)P in vitro and the 5-phosphatase domain is required for clathrin-mediated endocytosis in vivo. Supporting Evidence: PMID:24977345 increased the 5′-phosphatase activity of immunoprecipitated Synj in vitro PMID:34596663 These results indicate that Synj's 5′-PPase activity, or the ability to convert PI(4,5)P2 to PI(4)P, is essential for CME |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: Synj is a soluble cytoplasmic protein that acts on the cytoplasmic leaflet of presynaptic, endocytic and autophagosomal membranes, and also in non-neuronal wing-disc cells. Reason: Synj has no transmembrane segment or signal peptide. It acts in the cytoplasm of nerve terminals on synaptic vesicles and nascent autophagosomes, and it also acts in wing imaginal disc cells. Because it works in several cytoplasmic compartments in neuronal and non-neuronal cells, cytoplasm is the appropriate general location to inherit. FB:FBgn0034691 appearing among the IBA sources reflects FlyBase's own experimental localization of Synj. Supporting Evidence: PMID:14622578 We show that Synj is specifically localized to presynaptic terminals and is associated with synaptic vesicles. PMID:30541947 Using wingdiscs of Drosophila melanogaster, this study shows that Synaptojanin (Synj), a dual phosphatase, modulates PI(4)P levels and affects Smo activation |
| GO:0016020 membrane | IBA GO_REF:0000033 | MODIFY | Summary: Correct (peripheral membrane association) but general; the supported membrane is the vesicle membrane. Reason: Synj is a peripheral membrane protein. It associates with synaptic vesicles and newly formed endocytic vesicles, where Endophilin recruits it, and with nascent presynaptic autophagosomes. FlyBase records an IDA for vesicle membrane (GO:0012506) on this gene. That term covers both the endocytic and autophagosomal membranes Synj acts on, so it is proposed as the more specific replacement. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: PANTHER:PTN000127779 · PTN000127779 SUPPORTS TRANSFER Peripheral membrane association is inherited correctly by the synaptojanin/5-phosphatase clade and Synj is inside it; the MODIFY only sharpens the generic membrane term to the vesicle membranes on which fly Synj acts, and does not dispute the transfer. Proposed replacements: vesicle membrane Supporting Evidence: PMID:14622578 Endophilin recruits and stabilizes Synj on newly formed vesicles to promote vesicle uncoating. PMID:14622578 We show that Synj is specifically localized to presynaptic terminals and is associated with synaptic vesicles. |
| GO:0016791 phosphatase activity | IEA GO_REF:0000002 | MODIFY | Summary: Correct but uninformative. The two InterPro sources correspond to two distinct lipid phosphatase activities, and both should be stated. Reason: IPR000300 (IPPc) is the central inositol polyphosphate 5-phosphatase domain, which is directly shown to convert PI(4,5)P2 to PI(4)P in fly. IPR002013 is the SAC domain. SAC-like domains of synaptojanins and of yeast Inp52/Inp53 (same PANTHER subfamily SF257 as Synj) remove the 3- and 4-phosphates from PI(3)P, PI(4)P and PI(3,5)P2. The fly SAC catalytic CX5R(T/S) motif is intact, and fly Synj knockdown raises PI(4)P. Both specific activities replace the generic term. Proposed replacements: phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity phosphatidylinositol-4-phosphate phosphatase activity Supporting Evidence: PMID:24977345 increased the 5′-phosphatase activity of immunoprecipitated Synj in vitro PMID:10224048 Purified recombinant SAC1-like domains convert yeast lipids phosphatidylinositol (PI) 3-phosphate, PI 4-phosphate, and PI 3,5-bisphosphate to PI, whereas PI 4,5-bisphosphate is not a substrate. file:DROME/Synj/Synj-bioinformatics/RESULTS.md human CLDCLDRT (from residue 383) aligns to fly CLDCLDRT starting at fly residue 396, identical |
| GO:0045202 synapse | IEA GO_REF:0000044 | MODIFY | Summary: Correct but general; Synj is specifically presynaptic. Reason: Immunolocalization places Synj specifically in presynaptic terminals, at larval NMJ boutons and photoreceptor terminals. The gene already carries presynapse (GO:0098793), a part_of descendant of synapse, so that term is the specific replacement. Proposed replacements: presynapse Supporting Evidence: PMID:14622578 We show that Synj is specifically localized to presynaptic terminals and is associated with synaptic vesicles. |
| GO:0046856 phosphatidylinositol dephosphorylation | IEA GO_REF:0000002 | ACCEPT | Summary: Both catalytic domains dephosphorylate phosphatidylinositol phosphates; this is the direct metabolic process Synj carries out. Reason: Fly Synj dephosphorylates PI(4,5)P2 to PI(4)P (5-phosphatase domain), and its SAC domain controls PI(3)P/PI(3,5)P2 on autophagosomes and PI(4)P levels in wing discs. Synj itself performs the catalytic step, so this is participation, not an indirect effect. The term is as precise as a process term can be for an enzyme with several phosphoinositide substrates. Supporting Evidence: PMID:24977345 increased the 5′-phosphatase activity of immunoprecipitated Synj in vitro PMID:28331029 R258Q affects the synaptojanin SAC1 domain that dephosphorylates PI(3)P and PI(3,5)P2 |
| GO:0048488 synaptic vesicle endocytosis | IBA GO_REF:0000033 | ACCEPT | Summary: Core process, supported in fly by mutant physiology and ultrastructure and by domain-specific rescue. Reason: PTN000878538 is the synaptojanin clade node. It is seeded by fly Synj itself (the FlyBase IMP), worm unc-26, mouse Synj1 and human SYNJ1/SYNJ2, and Synj sits inside it. In fly, synj mutants have endocytic electrophysiological and ultrastructural defects, null synapses retain only about 10-20% of the wild-type endocytosis rate, and the 5-phosphatase activity is required for clathrin-mediated endocytosis. Synj also shapes bulk endocytosis and retrieval of different vesicle pools. The general term accurately covers participation across these retrieval modes, and the specific uncoating step is added separately as GO:0016191. Supporting Evidence: PMID:14622578 synj encodes a phosphatidylinositol phosphatase involved in clathrin-mediated endocytosis. PMID:16269341 Steady-state exocytosis rates reveal that endocytosis saturates in mutant neuromuscular terminals at approximately 80 vesicles/s, 10%-20% of the wild-type rate. PMID:34596663 These results indicate that Synj's 5′-PPase activity, or the ability to convert PI(4,5)P2 to PI(4)P, is essential for CME PMID:27559170 dynamic phosphorylation and dephosphorylation of Synj differentially maintain endocytosis of distinct functional synaptic vesicle pools |
| GO:0052658 inositol-1,4,5-trisphosphate 5-phosphatase activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Plausible inherited in vitro activity of the synaptojanin 5-phosphatase domain toward soluble Ins(1,4,5)P3; not the physiological substrate in fly. Reason: PAINT placed this term at PTN002597976, a node whose donors are synaptojanins (rat Synj1 and Synj2, human SYNJ1) and fission yeast Syj1. Fly Synj falls under the same synaptojanin clade, and its 5-phosphatase catalytic motifs are intact, so there is no evidence of loss. However, no fly experiment has tested soluble inositol trisphosphate, and every fly phenotype maps to membrane phosphoinositides (PI(4,5)P2, PI(4)P, PI(3)P). The inherited capability is kept as non-core rather than removed. Supporting Evidence: PMID:10224048 The 5-phosphatase domains of synaptojanin, Inp52p, and Inp53p are also catalytic file:DROME/Synj/Synj-bioinformatics/RESULTS.md human PAWTDRV (802) aligns to fly PAWTDRV (812), identical |
| GO:0098793 presynapse | IEA GO_REF:0000108 | ACCEPT | Summary: Presynaptic localization is directly established in fly. Reason: Synj is specifically localized to presynaptic terminals and associated with synaptic vesicles at larval NMJ boutons and photoreceptor terminals. Its presynaptic enrichment is the basis for its synaptic autophagy role. Supporting Evidence: PMID:14622578 We show that Synj is specifically localized to presynaptic terminals and is associated with synaptic vesicles. PMID:28331029 Synj is strongly enriched at presynaptic terminals |
| GO:0016191 synaptic vesicle uncoating | IMP PMID:14622578 Synaptojanin is recruited by endophilin to promote synaptic ... | NEW | Summary: Synj performs the PI(4,5)P2-hydrolysis step that releases clathrin adaptors during uncoating of endocytosed synaptic vesicles. Reason: Synj does part of the work of uncoating. Its 5-phosphatase removes the PI(4,5)P2 that anchors clathrin adaptors, and synj mutants accumulate coated vesicles. Comparator check (QuickGO, GO:0016191), looking at other genes in the same role. Worm unc-26 (IMP, PMID:10931870) and mouse Synj1 (IDA/IMP) carry this term, as does the uncoating cofactor auxilin (Dnajc6). The absence of the term on fly Synj is therefore a gap, not a convention. The term is a specific step within synaptic vesicle endocytosis, not a redundant ancestor of an existing term. Supporting Evidence: PMID:14622578 Endophilin recruits and stabilizes Synj on newly formed vesicles to promote vesicle uncoating. PMID:16269341 proteins that together function to uncoat vesicles in classical clathrin-mediated endocytosis PMID:27559170 is known to play an important role in vesicle recycling by promoting the uncoating of clathrin following synaptic vesicle uptake |
| GO:0043812 phosphatidylinositol-4-phosphate phosphatase activity | ISS PMID:10224048 SAC1-like domains of yeast SAC1, INP52, and INP53 and of hum... | NEW | Summary: SAC-domain phosphoinositide phosphatase activity, the second catalytic activity of synaptojanin. Reason: The SAC domain (PROSITE PS50275, residues 120-455) is conserved in fly Synj, including the catalytic CX5R(T/S) motif CLDCLDRT. SAC-like domains of human synaptojanin and of yeast Inp52/Inp53, which share PANTHER subfamily SF257 with Synj, dephosphorylate PI(4)P, PI(3)P and PI(3,5)P2. In fly, Synj knockdown raises PI(4)P in wing discs, and the SAC-domain R228Q knock-in blocks autophagosome maturation. The 5-phosphatase activity is already annotated but the SAC activity is not; this row adds the missing second catalytic activity. Supporting Evidence: PMID:10224048 Purified recombinant SAC1-like domains convert yeast lipids phosphatidylinositol (PI) 3-phosphate, PI 4-phosphate, and PI 3,5-bisphosphate to PI, whereas PI 4,5-bisphosphate is not a substrate. PMID:30541947 Using wingdiscs of Drosophila melanogaster, this study shows that Synaptojanin (Synj), a dual phosphatase, modulates PI(4)P levels and affects Smo activation file:DROME/Synj/Synj-bioinformatics/RESULTS.md human CLDCLDRT (from residue 383) aligns to fly CLDCLDRT starting at fly residue 396, identical |
| GO:0097352 autophagosome maturation | IMP PMID:28331029 The SAC1 domain in synaptojanin is required for autophagosom... | NEW | Summary: The SAC domain of Synj dephosphorylates PI(3)P/PI(3,5)P2 on nascent presynaptic autophagosomes, releasing Atg18a and allowing maturation. Reason: This is participation, not a downstream phenotype. Synj is present at the presynaptic terminal, and its SAC catalytic activity acts on the lipids of the nascent autophagosome membrane. An endogenous knock-in of a single SAC-domain residue (R228Q), which leaves 5-phosphatase function and endocytosis intact, traps the PI(3)P-binding protein Atg18a on autophagosomes and blocks their maturation. Synj therefore performs a lipid-remodelling step of maturation. It is a non-core role relative to vesicle recycling. Supporting Evidence: PMID:28331029 accumulate the PI(3)P/PI(3,5)P2-binding protein Atg18a on nascent synaptic autophagosomes, blocking autophagosome maturation at fly synapses PMID:28331029 Synaptojanin drives synaptic endocytosis by dephosphorylating PI(4,5)P2, but this function appears normal in SynaptojaninRQ knock-in flies. |
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Download this section (compressed HTML)Q: Does fly Synj hydrolyse soluble Ins(1,4,5)P3 at physiologically relevant rates, as the PAINT-inherited GO:0052658 implies, or is its 5-phosphatase effectively lipid-restricted in vivo?
Q: Is the SAC-domain activity of fly Synj demonstrable in vitro on PI(3)P versus PI(4)P, and does the R228Q substitution abolish it in the fly protein as in human SYNJ1?
Q: Should the Synj effect on Smoothened activation in wing discs (RNAi-only, single study) be captured as a regulation-of-Hedgehog-signalling annotation, or is it an indirect consequence of altered PI(4)P pools?
Experiment: Purify recombinant fly Synj SAC domain, wild type and R228Q, and measure phosphate release from PI(3)P, PI(4)P and PI(3,5)P2 by malachite green assay. This tests the transferred SAC specificity directly.
Experiment: Assay purified fly Synj 5-phosphatase domain on Ins(1,4,5)P3 and Ins(1,3,4,5)P4 alongside PI(4,5)P2 to establish whether the soluble-substrate activity inherited by IBA is retained.
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Download this section (compressed HTML)Synaptojanin (Synj) encodes a synaptic Phosphoinositide phosphate (PtdInsP) phosphatase that catalyzes the hydrolysis of phosphate groups from phosphorylated inositols. It is recruited or stabilized by the product of EndoA to endocytic membranes, and it catalyzes dephosphorylation reactions implicated in the uncoating of nascent endocytic vesicles. When the product of Synj dephosphorylates phosphoinositides on nascent vesicles, endocytic adaptors with affinity for these lipids will leave the membrane to uncoat the vesicle.
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