gbf-1 (C24H11.7, also called phi-34) encodes GBF-1, the C. elegans ortholog of mammalian GBF1, yeast Gea1/Gea2 and Drosophila Gartenzwerg. It is a large (1975-residue) peripheral membrane protein of the GBF1 subfamily of Sec7-domain guanine-nucleotide exchange factors for Arf GTPases, with N-terminal DCB/HUS regions, a central catalytic Sec7 domain (residues 624-812) and a long, largely disordered C-terminus. A short isoform (b) lacks the first 1490 residues, including the Sec7 domain. GBF-1 sits on the cis face of the Golgi mini-stacks, at the transitional ER-Golgi units that lie against ER exit sites in oocytes and intestine. By analogy with its orthologs, it activates Arf1-type GTPases there to recruit the COPI coat for retrograde transport from the cis-Golgi and ER-Golgi intermediate compartment back to the ER. Knockdown makes the Golgi stacks clump and fills them with vesicles at the cis face, collapses the ER lumen, and partly blocks secretion (caveolin, yolk, cuticle and eggshell components). It also disturbs intestinal early and late endosomes and mitochondrial morphology. The null mutant is lethal, and RNAi causes cuticle rupture, sterility and embryonic lethality. GBF-1 co-immunoprecipitates with the kinase SGK-1 and is needed for its basolateral localization in the intestine. No in vitro exchange assay has been reported for the worm protein.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000137 Golgi cis cisterna | IBA GO_REF:0000033 | ACCEPT | Summary: is_active_in cis-Golgi cisterna, from the GBF1 ortholog node PTN008503207 (seeds include Drosophila garz and gbf-1 itself). Reason: GBF-1 appears among its own IBA sources because WormBase has an IDA for this term from the same paper. That marks experimental grounding on the target. It is not circularity. The GBF1 node is orthologous, and gbf-1 is its only C. elegans member. The worm protein localizes to the cis face of the Golgi, where a GEF must act on the membrane. Core location. Supporting Evidence: PMID:23840591 GBF-1 is present on the cis-face of the Golgi at so-called transitional ER-Golgi elements PMID:23840591 we found that GBF-1 was recruited to the cis-Golgi independently of AGEF-1 |
| GO:0000137 Golgi cis cisterna | IDA PMID:23840591 The ArfGEF GBF-1 Is Required for ER Structure, Secretion and... | ACCEPT | Summary: Antibody staining in oocytes places GBF-1 between the medial-Golgi marker UGTP-1 and the ERES marker SEC-16, on the cis face of the Golgi mini-stacks. Reason: Direct localization with an affinity-purified peptide antibody whose signal is lost on gbf-1 RNAi. Triple labelling resolves the cis face. This is the main site of action. Core. Supporting Evidence: PMID:23840591 GBF-1 is present on the cis-face of the Golgi at so-called transitional ER-Golgi elements |
| GO:0005085 guanyl-nucleotide exchange factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: Guanine-nucleotide exchange factor activity inherited from the large-Sec7-GEF ancestral node (PTN008950430). Its seeds are characterised Sec7 GEFs, including yeast Gea1/Gea2 and Sec7, Drosophila garz and mammalian GBF1/BIG1/BIG2. Reason: GBF-1 has an intact Sec7 domain (residues 624-812) within the GBF1-subfamily architecture and sits inside the clade that inherited exchange activity, with no sign of loss. No in vitro assay exists for the worm protein, but the RNAi phenotypes (cis-Golgi vesicle accumulation, Golgi collapse, secretion defects) match loss of GBF1 Arf-GEF function in other systems. GO:0005086 ARF GEF activity has been merged into GO:0005085, so this is the most specific term available. Core. Supporting Evidence: file:worm/gbf-1/gbf-1-uniprot.txt InterPro; IPR000904; Sec7_dom. file:worm/gbf-1/gbf-1-uniprot.txt Guanine-nucleotide exchange factor (GEF) for members of the Arf family of small GTPases involved in trafficking in the early secretory pathway PMID:23840591 C. elegans PHI-34 is the closest homolog to mammalian GBF1 with 38% identity |
| GO:0005085 guanyl-nucleotide exchange factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the Sec7 domain signatures (IPR000904, IPR035999), which match GBF-1. Reason: Agrees with the IBA row. The Sec7 domain is the catalytic module of Arf GEFs, so the mapping holds for the full-length protein (isoform a). Isoform b lacks the Sec7 domain, but GOA annotates the canonical entry. Core. Supporting Evidence: file:worm/gbf-1/gbf-1-uniprot.txt InterPro; IPR000904; Sec7_dom. file:worm/gbf-1/gbf-1-deep-research-manual.md therefore lacks the Sec7 domain (624-812) |
| GO:0005793 endoplasmic reticulum-Golgi intermediate compartment | EXP PMID:23840591 The ArfGEF GBF-1 Is Required for ER Structure, Secretion and... | ACCEPT | Summary: UniProt-curated location from the same imaging, which places GBF-1 in the transitional ER-Golgi elements between ER exit sites and the Golgi. Reason: C. elegans germ cells have no separate ERGIC tubulovesicular cluster. The transitional ER-Golgi element, where GBF-1 sits between SEC-16 and UGTP-1, is the functional equivalent of the ERGIC/cis-Golgi interface. Mammalian GBF1 is also found on the ERGIC. The mapping is reasonable and agrees with the cis-Golgi IDA. EXP is an unusual code for a localization (IDA would be more usual), but the claim is sound. Supporting Evidence: PMID:23840591 GBF-1 is present on the cis-face of the Golgi at so-called transitional ER-Golgi elements file:worm/gbf-1/gbf-1-uniprot.txt Endoplasmic reticulum-Golgi intermediate compartment {ECO:0000269|PubMed:23840591} |
| GO:0005793 endoplasmic reticulum-Golgi intermediate compartment | IEA GO_REF:0000044 | ACCEPT | Summary: SubCell-vocabulary mapping of the UniProt curated location (ERGIC, from PMID:23840591). Reason: The row mechanically restates the curated UniProt location, which rests on the 2013 imaging. Consistent with the EXP row. Supporting Evidence: PMID:23840591 GBF-1 is present on the cis-face of the Golgi at so-called transitional ER-Golgi elements |
| GO:0005794 Golgi apparatus | IEA GO_REF:0000120 | ACCEPT | Summary: Golgi apparatus, from combined ARBA and SubCell mapping. Reason: Root organelle term on an electronic row, so I checked what it rests on. ARBA alone is not evidence, but the organelle claim holds on direct worm imaging, which places GBF-1 on the cis face of the Golgi mini-stacks. The organelle term stays informative beside the more specific cis-cisterna rows. Supporting Evidence: PMID:23840591 GBF-1 is present on the cis-face of the Golgi at so-called transitional ER-Golgi elements |
| GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: Retrograde Golgi-to-ER transport, inherited from the GBF1 ortholog node, seeded by human GBF1 (Q92538). Reason: GBF1 does the work of this process. It activates Arf on cis-Golgi/ERGIC membranes to recruit COPI, the first step of retrograde vesicle formation. Worm data agree. GBF-1 is on the cis-Golgi, and its knockdown causes vesicles to accumulate at the cis face, consistent with blocked recycling. The authors note that retrograde transport could not be measured directly in the whole animal. This is the core process. Supporting Evidence: PMID:23840591 GBF-1 should recruit ARF-1.2 to the Golgi and promote the formation of COPI-coated vesicles destined to the ER PMID:23840591 upon gbf-1(RNAi) numerous vesicles accumulated at the cis-Golgi, representing most likely ER-derived COPII vesicles PMID:23840591 retrograde transport in the ER-Golgi shuttle is not easily studied, and in particularly not in a whole animal |
| GO:0007005 mitochondrion organization | IMP PMID:25190516 The small GTPase Arf1 modulates mitochondrial morphology and... | KEEP AS NON CORE | Summary: gbf-1 RNAi gives enlarged, interconnected mitochondria and reduced mitochondrial activity in worms. The phenotype resembles ARF-1 loss and knockdown of ER-mitochondria contact-site components. Reason: Only the abstract is cached. The curator saw the full text, and the phenotype is reported clearly, so I defer to the IMP. The proposed mechanism is ARF-1 acting at ER-mitochondria contacts, independent of vesicle traffic. GBF-1's contribution would be the activating step for ARF-1. It is a secondary role, not the main function of the protein. Supporting Evidence: PMID:25190516 Loss of function of ARF-1 or GBF-1 impaired mitochondrial morphology and activity in Caenorhabditis elegans. PMID:25190516 similar mitochondrial abnormalities resulted from knockdown of either GBF-1 or contact site components in worms, suggesting that the role of Arf1 in mitochondrial functioning is linked to ER-mitochondrial contacts |
| GO:0007029 endoplasmic reticulum organization | IMP PMID:23840591 The ArfGEF GBF-1 Is Required for ER Structure, Secretion and... | KEEP AS NON CORE | Summary: gbf-1 RNAi disperses the reticular ER and collapses the ER lumen in oocytes, while ER exit sites are preserved. Reason: The phenotype is strong and specific (agef-1 RNAi has no ER effect), so the IMP stands. The authors themselves propose that the effect is indirect, a consequence of reduced retrograde membrane and lipid return to the ER. Non-core. Supporting Evidence: PMID:23840591 In gbf-1(RNAi) oocytes we observed a severely disturbed ER organization PMID:23840591 we would like to suggest that this effect is indirect and probably coupled through a decreased reflux of lipids |
| GO:0007030 Golgi organization | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Golgi organization, inherited from the GBF1 ortholog node (garz, human GBF1). Reason: True for the worm protein. gbf-1 RNAi makes the dispersed Golgi mini-stacks aggregate, and Golgi maintenance is a conserved GBF1 role. Golgi integrity is a consequence of balanced COPI-dependent traffic, which is the core activity, so I keep this as a non-core process. Supporting Evidence: PMID:23840591 gbf-1(RNAi) caused the small Golgi foci to aggregate into large structures PMID:23840591 We found that GBF-1 performs evolutionary conserved functions of GBF1/garz/Gea1-2 ArfGEF guanine nucleotide exchange factors, namely a role in retrograde transport from the Golgi to the ER, in Golgi maintenance and secretion. |
| GO:0016197 endosomal transport | IMP PMID:23840591 The ArfGEF GBF-1 Is Required for ER Structure, Secretion and... | KEEP AS NON CORE | Summary: In the intestine, gbf-1 RNAi reduces RAB-5 early-endosome signal and produces enlarged tubular RAB-7 late-endosome networks. Oocytes take up less yolk. Reason: The intestinal endosome phenotype is real and reported in the full text. The paper gives no direct transport measurement in the gut. In oocytes, receptor recycling and lysosomal degradation are normal, and the authors favour an indirect explanation for the reduced yolk uptake. GBF1 orthologs act on endosomes and the plasma membrane in other systems, so a direct role is plausible. Kept as non-core and not promoted. Supporting Evidence: PMID:23840591 GBF-1 might be required for maintenance of endosome morphology and potentially for efficient endocytic transport in the gut epithelium PMID:23840591 Therefore, the decrease in yolk uptake is not easily explained be a defect in receptor-mediated endocytosis. |
| GO:0032012 regulation of ARF protein signal transduction | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO process mapping from the Sec7 domain. Reason: An Arf GEF directly regulates Arf signalling by loading GTP. This is the standard process companion of the Sec7 GEF function and is accurate for GBF-1. Supporting Evidence: file:worm/gbf-1/gbf-1-uniprot.txt InterPro; IPR000904; Sec7_dom. PMID:23840591 GBF-1 should recruit ARF-1.2 to the Golgi and promote the formation of COPI-coated vesicles destined to the ER |
| GO:0046903 secretion | IMP PMID:23840591 The ArfGEF GBF-1 Is Required for ER Structure, Secretion and... | KEEP AS NON CORE | Summary: gbf-1 RNAi partially blocks caveolin export in oocytes and yolk export from the intestine. It also weakens the cuticle and eggshell, consistent with reduced secretion. Reason: The secretion defects are documented with several cargoes, so the IMP stands. The authors conclude that the role is likely indirect, a consequence of defective retrograde transport and Golgi integrity. The broad term is as precise as the mixed cargo data allow. Non-core. Supporting Evidence: PMID:23840591 Similar to the reported phenotype in agef-1(RNAi), we also observed a comparable partial effect on CAV-1 secretion in gbf-1(RNAi) oocytes PMID:23840591 However, this role is likely indirect through GBF-1's involvement in retrograde transport to the ER. |
| GO:0070971 endoplasmic reticulum exit site | IDA PMID:23840591 The ArfGEF GBF-1 Is Required for ER Structure, Secretion and... | KEEP AS NON CORE | Summary: GBF-1 staining partially overlaps the ERES marker SEC-16 in oocytes. Reason: The overlap is partial. Triple labelling puts GBF-1 between SEC-16 and the Golgi, that is, on the cis-Golgi side of the ERES-Golgi unit rather than on the ER exit site itself. The authors read the overlap as a sign that the two compartments lie very close together. The IDA is kept as a peripheral location. The core location is the cis-Golgi. Supporting Evidence: PMID:23840591 GBF-1 and SEC-16 partially overlap by confocal microscopy PMID:23840591 GBF-1 is present on the cis-face of the Golgi at so-called transitional ER-Golgi elements |
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Download this section (compressed HTML)Q: Which Arf paralogs does GBF-1 activate directly (ARF-1.2, ARF-3, ARF-5 or ARF-6)? The 2013 study assumes ARF-1.2, but no exchange assay has been done with the worm protein.
Q: Does isoform b (G5EGS5-2), which lacks the Sec7 domain, have any function, for example as a dominant-negative or scaffolding fragment?
Q: Is GBF-1's effect on intestinal endosomes (RAB-5 loss, tubular RAB-7 networks) direct, through endosomal Arf activation, or secondary to Golgi dysfunction? The same question applies to its role at ER-mitochondria contacts.
Q: Should the worm protein carry a COPI-coat recruitment process term, such as COPI coating of Golgi vesicles? It would describe the GEF's participation step, but no worm-specific coat-recruitment data exist yet.
Experiment: Purify the GBF-1 Sec7 domain (wild type and the glutamic-finger mutant) and measure GDP/GTP exchange on myristoylated ARF-1.2, ARF-3 and ARF-5 on liposomes, with and without brefeldin A, to define activity and substrate specificity.
Experiment: Tag endogenous GBF-1 by CRISPR and live-image COPI (e.g. GFP-tagged coatomer) recruitment to cis-Golgi membranes in oocytes, after auxin-induced GBF-1 degradation, to test directly whether GBF-1 drives coat assembly and retrograde transport in vivo.
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