SNF-12 is a multi-pass membrane protein of the SLC6 sodium/neurotransmitter symporter family expressed in the C. elegans epidermis (hypodermis). Its transport substrate has not been identified. SNF-12 is required cell autonomously in the epidermis for induction of the nlp-29 cluster of antimicrobial peptide (AMP) genes after infection by the fungus Drechmeria coniospora and after wounding, and for constitutive expression of caenacin (cnc) AMP genes. It is needed for both epidermal AMP-inducing pathways, the neuroendocrine TGF-beta pathway and the p38 MAPK pathway. Its C terminus binds the STAT-like transcription factor STA-2, and the two proteins act together downstream of the PKC/p38 MAPK (PMK-1) cascade to drive AMP transcription. SNF-12 resides in apical, endosome-like vesicular clusters of the epidermis that do not coincide with known endosomal, lysosomal or plasma-membrane markers; after wounding these clusters are recruited to the wound site in a microtubule-dependent manner. SNF-12 is thought to act as a vesicular signalling platform for STA-2 rather than through a known transport activity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002804 positive regulation of antifungal peptide production | IMP PMID:21575913 Unusual regulation of a STAT protein by an SLC6 family trans... | ACCEPT | Summary: snf-12 mutants fail to induce nlp-29 cluster AMP genes after infection by the fungus D. coniospora; SNF-12 acts cell autonomously in the epidermis together with STA-2. Reason: Direct IMP evidence (two alleles) from the paper that identified SNF-12 in an AMP-reporter screen. The NIPI-4 paper reconfirmed by qRT-PCR that nlp-29 induction after infection is abrogated in snf-12 mutants. SNF-12 binds STA-2 and is part of the signalling machinery, so it does part of the regulatory work. This is the core biological role of SNF-12. Supporting Evidence: PMID:21575913 we identify the sodium-neurotransmitter symporter SNF-12, a member of the solute carrier family (SLC6), as being essential for both these immune signaling pathways PMID:22470487 We could confirm by qRT-PCR that in the nipi-4(fr106) mutant, just as in sta-2 or snf-12 mutants [21], the induction of nlp-29 after infection was essentially abrogated. |
| GO:0005283 amino acid:sodium symporter activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA transfer of amino acid:sodium symporter activity from an SLC6 node seeded by glycine and proline transporters (SLC6A5, SLC6A9, SLC6A7) and SLC6A14. Reason: SNF-12 is an SLC6 family member and a sodium-coupled symporter activity is plausibly inherited, so I do not reject the PAINT node placement. However, no transport activity or substrate has been demonstrated for SNF-12. The epidermal immunity review states that it is predicted to transport a bioactive amine and that its endogenous substrate is unknown. Its documented role is in STA-2 signalling, not transport, so this inferred activity is kept as non-core. Supporting Evidence: PMID:26716073 SNF-12/SLC6 is predicted to be a transporter of a bioactive amine, but its endogenous substrate has yet to be identified. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular-location mapping to cytoplasm, reflecting SNF-12 in cytoplasmic vesicles. Reason: SNF-12 is a multi-pass membrane protein found on cytoplasmic vesicle-like structures, so "cytoplasm" is correct in the GO sense but uninformative. The vesicle and endocytic vesicle annotations describe its location better. Supporting Evidence: PMID:22470487 SNF-12 is found in endosome-like vesicles in the epidermis, where it may act as a signaling platform during the innate immune response. |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA transfer of plasma membrane localization from SLC6 family members. Reason: Most characterized SLC6 transporters act at the plasma membrane, which explains the IBA. For SNF-12, however, colocalization analyses with plasma-membrane lipid markers and endosome/lysosome markers found no colocalization. SNF-12 is in a yet-undefined apical membrane compartment and in endosome-like vesicles. There is no experimental support for SNF-12 being active at the plasma membrane. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000177662 SUPPORTS SOURCE BUT NOT TARGET Plasma-membrane activity is well grounded for canonical SLC6 neurotransmitter transporters, but SNF-12 resides in an apical vesicular compartment that does not colocalize with plasma-membrane lipid markers. Supporting Evidence: PMID:31995031 We performed colocalisation analyses between SNF-12::GFP and available vesicular and plasma membrane markers (early, late and recycling endosomes, lysosomes, plasma membrane lipids). PMID:31995031 This indicates that SNF-12 is in a yet-to-be defined apical membrane compartment. |
| GO:0015179 L-amino acid transmembrane transporter activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA transfer of L-amino acid transmembrane transporter activity from a Drosophila SLC6 node. Reason: Plausible family-level inference that has not been tested for SNF-12. The substrate is unknown and is predicted to be a bioactive amine rather than an amino acid. Kept as non-core for the same reasons as the symporter IBA. Supporting Evidence: PMID:26716073 SNF-12/SLC6 is predicted to be a transporter of a bioactive amine, but its endogenous substrate has yet to be identified. |
| GO:0016020 membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Membrane localization from the SLC6 domain (IPR000175) and UniProt multi-pass membrane annotation. Reason: SNF-12 has the 12-transmembrane SLC6 fold and localizes to membranous vesicular structures. The general term is correct. Supporting Evidence: PMID:31995031 This indicates that SNF-12 is in a yet-to-be defined apical membrane compartment. |
| GO:0030139 endocytic vesicle | IDA PMID:21575913 Unusual regulation of a STAT protein by an SLC6 family trans... | ACCEPT | Summary: SNF-12 localizes to endosome-like vesicles in the epidermis, which depend on dynamin (DYN-1). Reason: Experimental localization by the WormBase curator, who read the full text. Later papers by the same group describe the compartment as dyn-1-dependent endocytic or endosome-like vesicles. A 2020 study did not see colocalization with standard endosome markers, so the exact identity of the compartment is not settled. I defer to the curator's call. Supporting Evidence: PMID:26716073 SNF-12 physically interacts with the transcription factor STA-2 and they have been found to colocalise in dyn-1-dependent-endocytic vesicles PMID:22470487 We previously showed that SNF-12 is found in endosome-like vesicles, and that endocytosis is indispensable for the transcriptional response to infection [21]. |
| GO:0031982 vesicle | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to vesicle. Reason: Consistent with the experimental localization of SNF-12 to endosome-like vesicles. Supporting Evidence: PMID:22470487 SNF-12 is found in endosome-like vesicles in the epidermis, where it may act as a signaling platform during the innate immune response. |
| GO:0035725 sodium ion transmembrane transport | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA transfer of sodium ion transmembrane transport from SLC6 family members. Reason: Sodium co-transport is plausibly inherited across SLC6 transporters, and no evidence of loss exists for SNF-12. However, no transport by SNF-12 has been measured, and its documented role is in STA-2 signalling. Supporting Evidence: PMID:26716073 SNF-12/SLC6 is predicted to be a transporter of a bioactive amine, but its endogenous substrate has yet to be identified. |
| GO:0045177 apical part of cell | IDA PMID:21575913 Unusual regulation of a STAT protein by an SLC6 family trans... | ACCEPT | Summary: SNF-12 is located in clusters at the apical surface of the hyp7 epidermal syncytium. Reason: Experimental localization, confirmed by a later live-imaging study that placed SNF-12 clusters in an apical membrane compartment of the epidermis. Supporting Evidence: PMID:31995031 The SLC6 family member SNF-12 was a prime candidate, as we have previously shown that it is localized in clusters at the apical surface of the hyp7 syncytium |
| GO:0097677 STAT family protein binding | IPI PMID:21575913 Unusual regulation of a STAT protein by an SLC6 family trans... | ACCEPT | Summary: SNF-12 binds the STAT-like transcription factor STA-2 directly, through the SNF-12 C terminus. Reason: Direct physical interaction reported in the primary paper and annotated by the WormBase curator. This is the best-supported molecular property of SNF-12 and the mechanistic basis of its role in STA-2-driven AMP induction. Supporting Evidence: PMID:21575913 We also identify the STAT transcription factor-like protein STA-2 as a direct physical interactor of SNF-12 and show that the two proteins function together to regulate AMP gene expression in the epidermis PMID:22470487 This cascade acts upstream of the STAT-like transcription factor STA-2 that physically interacts with the C-terminus of the SLC6 transporter SNF-12 [21]. |
| GO:1902475 L-alpha-amino acid transmembrane transport | IEA GO_REF:0000108 | KEEP AS NON CORE | Summary: Inter-ontology inference from the IBA L-amino acid transmembrane transporter activity. Reason: Derived mechanically from an untested family-level MF inference. The substrate of SNF-12 is unknown. Supporting Evidence: PMID:26716073 SNF-12/SLC6 is predicted to be a transporter of a bioactive amine, but its endogenous substrate has yet to be identified. |
| GO:1903804 glycine import across plasma membrane | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA transfer of glycine import across plasma membrane from a node seeded by the glycine transporters GlyT1/SLC6A9 and GlyT2/SLC6A5. Reason: This IBA is substrate-specific (glycine) and location-specific (plasma membrane). SNF-12 sits in its own PANTHER subfamily (PTHR11616:SF324), and nothing suggests it is a glycine transporter. Its substrate is unknown and predicted to be a bioactive amine. Experimentally it is not detected at the plasma membrane. Too specific for what is known. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000907238 SUPPORTS SOURCE BUT NOT TARGET Glycine import is grounded in the GlyT1/GlyT2 seeds; SNF-12 has an unknown (predicted amine) substrate and is not detected at the plasma membrane, so a glycine- and plasma-membrane-specific process is too specific. Supporting Evidence: PMID:26716073 SNF-12/SLC6 is predicted to be a transporter of a bioactive amine, but its endogenous substrate has yet to be identified. PMID:31995031 This indicates that SNF-12 is in a yet-to-be defined apical membrane compartment. |
Loading supporting content…
Download this section (compressed HTML)Q: What is the transport substrate of SNF-12, and is transport activity needed for STA-2 activation, or does SNF-12 act purely as a scaffold?
Q: Does SNF-12 binding hold STA-2 inactive (as MUP-4 does at hemidesmosomes), or is it needed to activate STA-2 after PMK-1 signalling?
Experiment: Express SNF-12 in Xenopus oocytes or HEK cells and screen candidate amines and amino acids for sodium-dependent uptake. Test transport-dead substitutions (e.g. in the conserved sodium-binding sites) for rescue of nlp-29 induction in snf-12 mutants.
Experiment: Map how the SNF-12 C terminus binds STA-2, and test whether a binding-deficient SNF-12 rescues AMP induction after D. coniospora infection.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)