glo-1 encodes the Caenorhabditis elegans ortholog of the Rab32/Rab38 subfamily of Rab small GTPases. It is expressed in the intestine, where it associates with the limiting membrane of gut granules, the intestine-specific lysosome-related organelles (LROs) that store birefringent, autofluorescent material and Nile Red-stained lipid and coexist with conventional degradative lysosomes. In its GTP-bound form, activated by the GLO-3/CCZ-1 guanine nucleotide exchange factor (with help from LMD-2 and the ABCG transporter WHT-2), GLO-1 is required for gut granule biogenesis: it routes membrane protein cargo such as PGP-2 and CDF-2 away from conventional endolysosomes and toward gut granules, downstream of or in parallel with AP-3, BLOC-1 and HOPS, and restricts RAB-7 to conventional endolysosomes. glo-1 mutants lack gut granules and show downstream defects in fat staining, ascaroside metabolism and LRO-dependent stress and immune responses.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003924 GTPase activity | IBA GO_REF:0000033 | ACCEPT | Summary: GLO-1 is a Rab32/38-family small GTPase; GTPase activity is the conserved core activity of the Rab clade. Reason: The PAINT node PTN001292747 covers the Rab family, whose members are experimentally characterised GTPases. GLO-1 retains the P-loop (GKT25S) and the switch-II catalytic glutamine (WDISGQ71), and the predicted hydrolysis-deficient Q71L and GTP-binding-deficient T25N mutants behave as expected for an active Rab in rescue assays. No direct hydrolysis assay exists for GLO-1, but the inheritance of the activity is well grounded. Supporting Evidence: PMID:30419011 GLO-1 is a Rab32 family member and the conservation of G-motifs suggests that it functions as a GTPase [21, 22]. PMID:30419011 Expression of GFP::GLO-1(Q71L), which is predicted to lack GTP hydrolysis and maintain an active GTP-bound conformation [59], was able to functionally replace GLO-1(+) (Fig 5D and Tables 1 and 2). PMID:30419011 Whereas glo-1(+) wild-type and glo-1(Q71L) mutant transgenes restored birefringent, PGP-2-containing, and autofluorescent gut granules when expressed in glo-1(-) mutants, the glo-1(T25N) mutant did not. |
| GO:0003924 GTPase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Rab family membership (InterPro IPR001806/IPR030697, UniRule) supports GTPase activity; consistent with the IBA row. Reason: Same claim as the IBA row; the electronic mapping from Rab-family signatures is sound for a Rab with intact G motifs. Supporting Evidence: file:worm/glo-1/glo-1-uniprot.txt Belongs to the small GTPase superfamily. Rab family. PMID:30419011 GLO-1 is a Rab32 family member and the conservation of G-motifs suggests that it functions as a GTPase [21, 22]. |
| GO:0005525 GTP binding | IEA GO_REF:0000120 | ACCEPT | Summary: GTP binding is required for GLO-1 function and GLO-1 undergoes GEF-stimulated nucleotide exchange in vitro. Reason: T25N (predicted to disrupt GTP binding) abolishes rescue; Q71L (GTP-locked) rescues; GLO-3-CCZ-1 catalyse Mant-GDP exchange on purified GLO-1. GTP binding is intrinsic to the GTPase cycle and is part of the core function. Supporting Evidence: PMID:30419011 Whereas glo-1(+) wild-type and glo-1(Q71L) mutant transgenes restored birefringent, PGP-2-containing, and autofluorescent gut granules when expressed in glo-1(-) mutants, the glo-1(T25N) mutant did not. PMID:30419011 Similar to other Rabs [29, 31], we show that the GTP bound form of GLO-1 is active in gut granule formation (Fig 5). PMID:39078368 LMD-2 thus promotes the GEF activity of the GLO-3–CCZ-1 complex to activate GLO-1. PMID:39078368 The reduction of Mant-GDP fluorescence with time is used to indicate nucleotide exchange. |
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | MODIFY | Summary: Cytoplasm is true but uninformative; GLO-1 is on the gut granule membrane. Reason: ARBA-derived cytoplasm row. GLO-1 is a peripheral Rab that cycles between cytosol and membranes; its experimentally established location is the gut granule membrane (GO:0044841), which GO places within cytoplasm (gut granule part_of/is_a cytoplasmic vesicle). Refine to the gut granule membrane term the gene already carries by IDA. Proposed replacements: gut granule membrane Supporting Evidence: PMID:22916203 (I) GFP::GLO-1 marked the periphery of gut granules in wild type (white arrows). PMID:30419011 Inactive Rabs are GDP-bound and can be extracted from organelle membranes into the cytosol by Rab GDI, while activated, GTP-bound Rabs are resistant to extraction and membrane localized [29, 31]. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: No evidence places C. elegans GLO-1 at mitochondria; the IBA derives from mammalian RAB32/RAB38 and Drosophila lightoid. Reason: This IBA is a root-organelle synthesis row. The node PTN000636119 is seeded by human RAB32 (Q13637), RAB38 (P57729), RAB29 (O14966) and fly lightoid; mammalian RAB32 mitochondrial association is a specialised property not reported for GLO-1. All imaging of GLO-1 in worms places it on gut granules, so the mitochondrion claim does not hold for this gene and is an over-propagation. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000636119 · Rab32/38/29 clade node SUPPORTS SOURCE BUT NOT TARGET Mitochondrial localization is documented for mammalian RAB32 seeds; GLO-1 localization data in C. elegans show gut granule association only. UniProtKB:Q13637 · human RAB32 SUPPORTS SOURCE BUT NOT TARGET RAB32 mitochondria/MAM association is not mirrored by worm GLO-1, which acts on intestinal LROs. Supporting Evidence: PMID:15843430 We show that the glo-1 gene encodes a predicted Rab GTPase that localizes to lysosome-related gut granules in the intestine PMID:22916203 (I) GFP::GLO-1 marked the periphery of gut granules in wild type (white arrows). |
| GO:0005794 Golgi apparatus | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Golgi localization is a Rab29 property mapped from the shared Rab29/32/38 InterPro entry; not reported for GLO-1. Reason: InterPro2GO from IPR030697 (Rab29/Rab38/Rab32). The Golgi claim reflects RAB29; GLO-1 is a Rab32/38 ortholog and has only been observed on gut granules. The root-organelle claim does not hold on present evidence. Supporting Evidence: file:worm/glo-1/glo-1-uniprot.txt InterPro; IPR030697; Rab29/Rab38/Rab32. PMID:22916203 GLO-1, which is orthologous to Rab32/38 in mammals [4], is localized to, and required for, gut granule biogenesis. |
| GO:0005802 trans-Golgi network | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: TGN localization rests on a single human RAB29 seed; GLO-1 has not been seen at the TGN. Reason: Node PTN000636041 is seeded by human RAB29 (O14966), a Golgi/TGN Rab. GLO-1 is in the Rab32/38 lineage and all localization data place it on gut granules. Over-propagation of a paralog-specific location. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG COMPARTMENT OR COMPLEX MISMATCH Sources checked: UniProtKB:O14966 · human RAB29 (RAB7L1) SUPPORTS SOURCE BUT NOT TARGET RAB29 TGN localization is well established, but GLO-1 belongs to the Rab32/38 subgroup and localizes to gut granules. PANTHER:PTN000636041 · Rab29/32/38 clade node SUPPORTS SOURCE BUT NOT TARGET Node placement extends a RAB29 location across the whole clade. Supporting Evidence: PMID:22916203 GLO-1, which is orthologous to Rab32/38 in mammals [4], is localized to, and required for, gut granule biogenesis. PMID:22916203 (I) GFP::GLO-1 marked the periphery of gut granules in wild type (white arrows). |
| GO:0005802 trans-Golgi network | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: Same TGN claim from the shared Rab29/32/38 InterPro/UniRule mapping; not supported for GLO-1. Reason: Consistent with the IBA TGN row: the mapping reflects RAB29 biology, and GLO-1 is observed only on gut granules. Supporting Evidence: file:worm/glo-1/glo-1-uniprot.txt InterPro; IPR030697; Rab29/Rab38/Rab32. PMID:22916203 GLO-1, which is orthologous to Rab32/38 in mammals [4], is localized to, and required for, gut granule biogenesis. |
| GO:0006886 intracellular protein transport | IBA GO_REF:0000033 | ACCEPT | Summary: GLO-1 directs protein cargo (e.g. PGP-2, CDF-2) to gut granules; intracellular protein transport is a fitting, appropriately specific process. Reason: Rab-family IBA, and the worm data support it directly: glo-1 loss mistraffics gut granule membrane proteins, and GLO-1 routes protein cargo away from conventional endolysosomes toward gut granules. GO has no more specific term for protein transport to lysosome-related organelles. Supporting Evidence: PMID:30419011 Notably, we did not detect a significant role for GLO-1 in the transport of cargo through conventional endolysosomes and instead show that GLO-1 functions to direct protein cargo away from this pathway toward gut granules (Figs 2 and 3). |
| GO:0007040 lysosome organization | IMP PMID:15843430 Genetic analysis of lysosomal trafficking in Caenorhabditis ... | MODIFY | Summary: glo-1(zu437) mutants lack gut granules; the process is biogenesis of a lysosome-related organelle, best captured by gut granule assembly. Reason: The IMP is sound in essence: gut granules are LROs and glo-1 mutants fail to form them. GO, however, places gut granule assembly (GO:1902900) under vesicle/organelle assembly, not under lysosome organization, and glo-1 loss does not significantly disturb conventional endolysosome biogenesis. Gut granule assembly is the more accurate term; this is a lateral refinement, not a correction of a mistaken annotation. Full text of PMID:15843430 was not accessible, but the abstract and later full-text papers establish the gut granule loss phenotype. Proposed replacements: gut granule assembly Supporting Evidence: PMID:15843430 The intestinal cells of Caenorhabditis elegans embryos contain prominent, birefringent gut granules that we show are lysosome-related organelles. PMID:15843430 We show that the glo-1 gene encodes a predicted Rab GTPase that localizes to lysosome-related gut granules in the intestine PMID:22916203 GLO-1, which is orthologous to Rab32/38 in mammals [4], is localized to, and required for, gut granule biogenesis. PMID:30419011 However, GLO-3 and GLO-1 do not function in endolysosome biogenesis like CCZ-1 and instead act to restrict RAB-7 to conventional endolysosomes. |
| GO:0012505 endomembrane system | IBA GO_REF:0000033 | MODIFY | Summary: Endomembrane system is correct but very general; GLO-1 acts on the gut granule membrane. Reason: Rab-family IBA, true for GLO-1. The specific supported location is the gut granule membrane (GO:0044841), already carried by IDA. GO does not formally link gut granule membrane to endomembrane system, so this is a refinement to the experimentally established compartment rather than to a graph descendant. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN001292747 · Rab family node SUPPORTS TRANSFER Endomembrane association is a general Rab property and transfers correctly, but is less specific than the gut granule membrane IDA. Proposed replacements: gut granule membrane Supporting Evidence: PMID:22916203 (I) GFP::GLO-1 marked the periphery of gut granules in wild type (white arrows). |
| GO:0016020 membrane | IEA GO_REF:0000044 | MODIFY | Summary: Membrane (from UniProt subcellular location) is correct but generic; refine to gut granule membrane. Reason: GLO-1 is a prenylated Rab associated with the gut granule limiting membrane; gut granule membrane is a descendant of membrane and is carried by IDA. Proposed replacements: gut granule membrane Supporting Evidence: PMID:22916203 (I) GFP::GLO-1 marked the periphery of gut granules in wild type (white arrows). |
| GO:0016192 vesicle-mediated transport | IEA GO_REF:0000002 | ACCEPT | Summary: As a Rab directing cargo delivery to gut granules, GLO-1 participates in vesicle-mediated transport. Reason: InterPro2GO from the Rab29/32/38 family; consistent with GLO-1 acting with AP-3, BLOC-1 and HOPS-dependent delivery of cargo to gut granules. No GO child specific for transport to lysosome-related organelles other than melanosomes exists, so this is as precise as the evidence allows. Supporting Evidence: PMID:30419011 Notably, we did not detect a significant role for GLO-1 in the transport of cargo through conventional endolysosomes and instead show that GLO-1 functions to direct protein cargo away from this pathway toward gut granules (Figs 2 and 3). PMID:22916203 GLO-1, which is orthologous to Rab32/38 in mammals [4], is localized to, and required for, gut granule biogenesis. |
| GO:0019915 lipid storage | IMP PMID:17202409 Function of the Caenorhabditis elegans ABC transporter PGP-2... | MARK AS OVER ANNOTATED | Summary: Loss of Nile Red-stained fat in glo-1 mutants reflects absence of the gut granule compartment rather than a role of GLO-1 in lipid storage. Reason: Only the abstract of PMID:17202409 is cached. It shows gut granules are sites of Nile Red-stained fat, but also that triacylglyceride levels are relatively normal in gut granule-deficient animals. The glo-1 phenotype is thus a downstream consequence of losing the organelle, not evidence that GLO-1 performs lipid storage. Supporting Evidence: PMID:17202409 We show that gut granules are sites of fat storage in C. elegans embryos and adults. PMID:17202409 Notably, levels of triacylglycerides are relatively normal in animals defective in the formation of gut granules. |
| GO:0031982 vesicle | IEA GO_REF:0000002 | MODIFY | Summary: Vesicle is correct but generic; GLO-1 is on gut granules. Reason: Gut granule (GO:0044840) is an is_a descendant of vesicle (via cytoplasmic vesicle) and is carried by IDA. Proposed replacements: gut granule Supporting Evidence: PMID:15843430 We show that the glo-1 gene encodes a predicted Rab GTPase that localizes to lysosome-related gut granules in the intestine PMID:22916203 (I) GFP::GLO-1 marked the periphery of gut granules in wild type (white arrows). |
| GO:0044840 gut granule | IDA PMID:15843430 Genetic analysis of lysosomal trafficking in Caenorhabditis ... | ACCEPT | Summary: GLO-1 localizes to gut granules, the intestinal lysosome-related organelles. Reason: Directly observed in PMID:15843430 (abstract) and confirmed by GFP::GLO-1 imaging in several full-text papers; GLO-1::GFP is routinely used as a gut granule/LRO marker. Supporting Evidence: PMID:15843430 We show that the glo-1 gene encodes a predicted Rab GTPase that localizes to lysosome-related gut granules in the intestine PMID:22916203 (I) GFP::GLO-1 marked the periphery of gut granules in wild type (white arrows). PMID:23705068 Both LMP-1::GFP (A–D) and GLO-1::GFP are lysosomal markers in C. elegans. |
| GO:0044841 gut granule membrane | IDA PMID:22916203 C. elegans BLOC-1 functions in trafficking to lysosome-relat... | ACCEPT | Summary: GFP::GLO-1 marks the periphery of gut granules, consistent with association with the limiting membrane. Reason: Imaging in PMID:22916203 shows GFP::GLO-1 at the gut granule periphery; GTP-bound Rabs are membrane-associated. This is the site of GLO-1 action. Supporting Evidence: PMID:22916203 (I) GFP::GLO-1 marked the periphery of gut granules in wild type (white arrows). PMID:30419011 Inactive Rabs are GDP-bound and can be extracted from organelle membranes into the cytosol by Rab GDI, while activated, GTP-bound Rabs are resistant to extraction and membrane localized [29, 31]. |
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Download this section (compressed HTML)Q: What are the GLO-1 effectors on gut granules, and do they include homologs of the mammalian Rab32/38 effectors VARP (ANKRD27) or the HOPS/AP-3 machinery?
Q: Is there a GLO-1-specific GAP that terminates its activity, and does GLO-1 GTP hydrolysis occur at measurable rates in vitro?
Q: Does GLO-1 ever associate with mitochondria or the Golgi in C. elegans tissues outside the intestine, as mammalian RAB32 and RAB29 do?
Experiment: Measure intrinsic and GAP-stimulated GTP hydrolysis of purified GLO-1 wild type and Q71L, and identify GTP-dependent GLO-1 interactors by affinity purification from intestinal lysates.
Hypothesis: GLO-1 is a catalytically active Rab whose GTP-bound form recruits specific effectors that sort cargo to gut granules.
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