agef-1 (Y6B3A.1) encodes AGEF-1, the single C. elegans member of the BIG subfamily of Sec7-domain guanine-nucleotide exchange factors for ADP-ribosylation factor (Arf) GTPases. It is orthologous to yeast Sec7p and human BIG1 (ARFGEF1) and BIG2 (ARFGEF2). The 1594-residue protein has the conserved DCB, HUS, Sec7 (catalytic), HDS and C-terminal domains of the family and no transmembrane segment. It acts at the trans-Golgi network, where it activates class I/II Arfs (ARF-1.2, ARF-3, ARF-1, ARF-5 in genetic studies) to drive AP-1-dependent cargo sorting and post-Golgi secretory transport. Loss of function inflates trans-Golgi cisternae, traps caveolin bodies in the Golgi, and impairs secretion from muscle and intestine. It also enlarges late endosomes/lysosomes in coelomocytes and increases basolateral LET-23 EGFR in vulval precursor cells, which enhances vulval induction. In the epidermis it acts upstream of RAB-35 to tune neuron-epidermal attachment, and the human BIG2 cDNA can substitute for it there. A catalytically dead Sec7 mutant acts as a dominant negative, so these roles depend on Arf exchange activity. No in vitro exchange assay has been reported for the worm protein.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005085 guanyl-nucleotide exchange factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: Guanine-nucleotide exchange factor activity inherited from the Sec7/BIG ancestral node (PTN008950430). AGEF-1 carries a complete Sec7 domain (residues 506-695) within the DCB-HUS-Sec7-HDS architecture of the BIG1/BIG2/Sec7p subfamily. Reason: The PAINT node is seeded by experimentally characterised Sec7 GEFs (yeast Sec7p, Gea1/Gea2, human BIG1/BIG2 and GBF1), and AGEF-1 sits inside the BIG clade with no sign of losing the catalytic domain. Worm in vivo evidence agrees. A Sec7 glutamic-finger mutant (E608K, matching the catalytically dead BIG2 E738K) acts as a dominant negative and phenocopies loss of agef-1, and human BIG2 rescues the mutant. No in vitro exchange assay exists for the worm protein. GO:0005086 ARF GEF activity has been merged into GO:0005085, so this is the most specific term available. Core function. Supporting Evidence: file:worm/agef-1/agef-1-uniprot.txt InterPro; IPR000904; Sec7_dom. PMID:25329472 BIG1 and BIG2 are Sec7 domain containing guanine nucleotide exchange factors (GEFs) for class I Arf GTPases PMID:42312793 To test this notion, we engineered a dominant negative agef-1 cDNA (AGEF-1[E608K]), which mimics a previously validated mutation in BIG2 that renders the SEC7 domain catalytically inactive PMID:42312793 We then overexpressed this mutated gene within the epidermis (SKIN::mCherry::AGEF-1[E608K]) of tbc-10; vdSi2 animals, and found that it suppressed the PLM axon breaks, phenocopying agef-1(vd123); tbc-10; vdSi2 animals PMID:42312793 Importantly, we found that SKIN::BIG2 fully restored the penetrance of PLM axon breaks |
| GO:0005085 guanyl-nucleotide exchange factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the Sec7 domain signatures (IPR000904, IPR035999), which match AGEF-1. Reason: Agrees with the IBA row and with the in vivo dominant-negative and BIG2-rescue evidence. The Sec7 domain is the catalytic module of all Arf GEFs, so this domain-to-function mapping is sound here. Core. Supporting Evidence: file:worm/agef-1/agef-1-uniprot.txt InterPro; IPR000904; Sec7_dom. PMID:42312793 To test this notion, we engineered a dominant negative agef-1 cDNA (AGEF-1[E608K]), which mimics a previously validated mutation in BIG2 that renders the SEC7 domain catalytically inactive |
| GO:0005794 Golgi apparatus | IEA GO_REF:0000120 | ACCEPT | Summary: Golgi apparatus, from ARBA plus the UniProt subcellular-location vocabulary. Reason: This is a root organelle term, and the row is an electronic synthesis, so I checked what it rests on. The source is ARBA, which is not evidence in itself. The organelle claim holds on two independent lines. The IBA trans-Golgi network row is seeded by BIG1/BIG2/Sec71 TGN localization, and agef-1 RNAi in worm oocytes gives a trans-Golgi phenotype (inflated cisternae, TGN exit block). No worm study has imaged AGEF-1 on the Golgi directly. The organelle term stays informative and is kept beside the more specific TGN row. Supporting Evidence: PMID:23840591 agef-1(RNAi) resulted in large inflated cisternae, consistent with a block in secretion at the trans-Golgi PMID:23840591 GBF-1 mainly acts at the cis-Golgi, while AGEF-1 is more important at the trans-Golgi. |
| GO:0005802 trans-Golgi network | IBA GO_REF:0000033 | ACCEPT | Summary: is_active_in trans-Golgi network, from the BIG1/BIG2 ortholog node PTN002240728 (seeds: rat BIG1/BIG2 and Drosophila Sec71). Reason: The node is orthologous rather than paralogous, and AGEF-1 is its only C. elegans member. Worm data put AGEF-1 function at the trans-Golgi. agef-1 RNAi inflates Golgi cisternae, consistent with a TGN exit block, and contrasts with the cis-Golgi defect of the GBF-1 paralog. The is_active_in qualifier fits a GEF that must act on the TGN membrane. Core location. Supporting Evidence: PMID:23840591 agef-1(RNAi) resulted in large inflated cisternae, consistent with a block in secretion at the trans-Golgi PMID:23840591 GBF-1 mainly acts at the cis-Golgi, while AGEF-1 is more important at the trans-Golgi. PMID:25329472 elegans homolog of the yeast Sec7p and human BIG1 and BIG2 Arf GEFs, which function with class I Arf GTPases and the AP-1 complex to regulate cargo sorting and trafficking from the TGN |
| GO:0016020 membrane | IEA GO_REF:0000044 | MODIFY | Summary: Membrane, from the UniProt subcellular-location vocabulary (ARBA-derived "Membrane"). Reason: This is true but uninformative. AGEF-1 has no transmembrane segment. Like BIG1/BIG2 it is a peripheral membrane protein that works on the TGN membrane, where it activates Arfs and recruits AP-1. The gene already carries trans-Golgi network by IBA, and the worm phenotypes are trans-Golgi phenotypes. Tagged epidermal AGEF-1 is in puncta at the cytoplasm and membrane. The specific membrane supported is the trans-Golgi network membrane. Proposed replacements: trans-Golgi network membrane Supporting Evidence: PMID:42312793 We found that epidermal AGEF-1::GFPx7 and AGEF-1[S784L]::GFPx7 localized to small puncta throughout the cytoplasm and membrane of the epidermis PMID:23840591 GBF-1 mainly acts at the cis-Golgi, while AGEF-1 is more important at the trans-Golgi. PMID:25329472 elegans homolog of the yeast Sec7p and human BIG1 and BIG2 Arf GEFs, which function with class I Arf GTPases and the AP-1 complex to regulate cargo sorting and trafficking from the TGN |
| GO:0016192 vesicle-mediated transport | IBA GO_REF:0000033 | MODIFY | Summary: Vesicle-mediated transport, from the Sec7-family node PTN008950430. Reason: This is correct but too general. For the BIG subfamily the established process is post-Golgi transport from the TGN. AGEF-1 does a step of it: it loads GTP onto Arfs, which recruit AP-1/clathrin coats to TGN membranes. This is participation, not only necessity. Worm loss-of-function blocks Golgi exit of caveolin bodies and secretion of ssGFP and yolk, which matches that step. Golgi to plasma membrane transport (GO:0006893, a descendant via post-Golgi vesicle-mediated transport) is the best-supported refinement. It is also the process the human ortholog ARFGEF2 carries as core. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN008950430 · Sec7-family ancestral node SUPPORTS TRANSFER The node spans BIG, GBF1 and other Sec7 GEFs whose shared process is vesicle-mediated transport. AGEF-1 is inside the BIG clade, where the transport step is post-Golgi (TGN to plasma membrane and endosomes). The transfer is sound but too coarse for this subfamily. Proposed replacements: Golgi to plasma membrane transport Supporting Evidence: PMID:23840591 In the absence of AGEF-1 or ARF-1.2, the internal CAV-1 structures become trapped in a perinuclear Golgi compartment PMID:25329472 Consistent with yeast Sec7p and human BIG1/BIG2 functioning in the secretory pathway, we found that agef-1(vh4) animals had defects in secretion of ssGFP from body wall muscles and Yolk::GFP from the intestine. PMID:25329472 elegans homolog of the yeast Sec7p and human BIG1 and BIG2 Arf GEFs, which function with class I Arf GTPases and the AP-1 complex to regulate cargo sorting and trafficking from the TGN |
| GO:0032012 regulation of ARF protein signal transduction | IEA GO_REF:0000002 | ACCEPT | Summary: Regulation of ARF protein signal transduction, from the Sec7 domain InterPro2GO mapping. Reason: An Arf GEF directly regulates Arf signalling by converting Arf-GDP to Arf-GTP. Worm genetics put AGEF-1 together with class I/II Arfs (ARF-1.2, ARF-3, ARF-1, ARF-5). The dominant-negative Sec7 mutant shows that the exchange activity is what matters in vivo. This matches the treatment of the human ortholog ARFGEF2. Supporting Evidence: PMID:25329472 In accordance with AGEF-1 being an Arf GEF, we found that ARF-1.2 and ARF-3, Class I/II Arf GTPases, also negatively regulate LET-23 EGFR signaling. PMID:42312793 To test this notion, we engineered a dominant negative agef-1 cDNA (AGEF-1[E608K]), which mimics a previously validated mutation in BIG2 that renders the SEC7 domain catalytically inactive |
| GO:0048471 perinuclear region of cytoplasm | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: Perinuclear region of cytoplasm, from the UniProt subcellular-location vocabulary (ARBA-derived). Reason: The perinuclear concentration of BIG1/BIG2 in mammalian cells reflects the pericentriolar Golgi ribbon. C. elegans has no ribbon: its Golgi is dispersed mini-stacks next to ER exit sites. Endogenously tagged epidermal AGEF-1 is in puncta throughout the cytoplasm, not perinuclear. The only "perinuclear" worm observation is a phenotype: in agef-1 loss of function, cargo becomes trapped in a perinuclear Golgi compartment. That describes the cargo, not the location of AGEF-1. The source is an ARBA prediction, which is not evidence. The term is not impossible, but nothing supports it for this protein. Supporting Evidence: PMID:23840591 The Golgi in C. elegans germ line is organized in small mini stacks localized in close proximity to ER-exit sites (ERES). PMID:42312793 We found that epidermal AGEF-1::GFPx7 and AGEF-1[S784L]::GFPx7 localized to small puncta throughout the cytoplasm and membrane of the epidermis PMID:23840591 In the absence of AGEF-1 or ARF-1.2, the internal CAV-1 structures become trapped in a perinuclear Golgi compartment file:worm/agef-1/agef-1-deep-research-manual.md C. elegans Golgi is dispersed in mini-stacks rather than a perinuclear ribbon |
Loading supporting content…
Download this section (compressed HTML)Q: Which Arf paralogs does AGEF-1 activate directly? Genetic data implicate ARF-1.2/ARF-1, ARF-3 and ARF-5, but no exchange assay has been done with the worm protein.
Q: Does AGEF-1 act on RAB-35 directly (as Sec7p acts as a Ypt effector), or only through an Arf intermediate such as ARF-5 stimulating the RAB-35 GEF RME-4/DENND1?
Q: Should WormBase capture the published agef-1 mutant and RNAi phenotypes (secretion, LET-23 EGFR basolateral localization, lysosome size) as GO process annotations? They currently have no experimental GO rows. Under the participation criterion, only the trafficking steps where the GEF acts would qualify, not the downstream signalling outcomes.
Experiment: Purify the AGEF-1 Sec7 domain (with and without the E608K glutamic-finger mutation) and measure GDP/GTP exchange on myristoylated ARF-1.2, ARF-3, ARF-5 and RAB-35 on liposomes, to define substrate specificity.
Experiment: Co-image endogenously tagged AGEF-1 with TGN (e.g. AP-1/APM-1), Golgi and recycling-endosome markers in intestine and epidermis, to place the protein directly rather than by phenotype.
Loading supporting content…
Download this section (compressed HTML)agef-1 encodes a putative ARF guanine nucleotide exchange factor orthologous to human ARFGEF1 (OMIM:604141) and ARFGEF2 (OMIM:605371); agef-1(RNAi) inhibits CAV-1 body formation in oocytes more severely than arf-1 disruption alone, indicating that activation of both ARF-1 and ARF-3 by AGEF-1 may be required for transport of caveolin from Golgi to CAV-1 bodies during oogenesis; more generally, AGEF-1 is required in mass RNAi assays for embryonic and larval viability, embryonic osmotic integrity, normal neurotransmission, locomotion, and osmoregulation, and normally rapid growth.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)