ARL5A (ADP-ribosylation factor-like protein 5A) is a small GTPase of the ARF (ADP-ribosylation factor) family in the Ras superfamily. It functions as a molecular switch cycling between inactive GDP-bound and active GTP-bound states, with GTP hydrolysis as its primary enzymatic activity. ARL5A is predominantly localized to the trans-Golgi network (TGN), where it is recruited by the upstream GTPase ARFRP1 in complex with the transmembrane protein SYS1. In its GTP-bound state, ARL5A recruits effector proteins including the GARP tethering complex (VPS51/52/53/54), ARMH3, and phosphatidylinositol 4-kinase beta (PI4KB). Through GARP recruitment, ARL5A promotes SNARE-dependent fusion of endosome-derived retrograde transport carriers with the TGN membrane, enabling recycling of TGN-resident proteins such as TGN46, mannose-6-phosphate receptors, furin, and sortilin. Through the ARMH3-PI4KB axis, ARL5A promotes synthesis of phosphatidylinositol 4-phosphate (PI4P) at the TGN, a critical signaling lipid for membrane trafficking and organelle identity. ARL5A also localizes to endolysosomal compartments, where it interacts with the Ragulator complex (LAMTOR1-5) in an amino acid-sensitive manner, linking nutrient sensing to retrograde trafficking independently of the Rag GTPase-mTORC1 pathway. ARL5 is conserved across eukaryotes and was present in the last eukaryotic common ancestor (LECA). No Xenopus tropicalis-specific functional studies have been reported; the protein's roles are inferred from its strong orthology with mammalian ARL5A/ARL5B, which have been characterized in detail through proximity labeling, knockout studies, and live-cell imaging.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic annotation of cytoplasm localization based on broad Arf-family orthology. ARL5A is a soluble protein that associates with membranes via an N-terminal amphipathic helix; it is expected to be present in the cytoplasm when in its GDP-bound (inactive) state, prior to membrane recruitment. However, cytoplasm is an extremely broad term and does not capture the functionally relevant localization of ARL5A at the TGN and endolysosomes. Reason: The annotation is not incorrect -- ARL5A is a peripheral membrane protein that cycles through the cytoplasm -- but it is too broad to be informative about the actual site of action. The functionally meaningful localization is at the trans-Golgi network and endolysosomes. Kept as non-core rather than removed because cytoplasmic localization of the GDP-bound pool is biologically real. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000917851 · PAINT node asserting cytoplasm across the Arf/Arl family SUPPORTS TRANSFER Deep node (PAINT snapshot 20260828) seeded across plants, fungi, animals and Dictyostelium. Every Arf-family GTPase has a soluble GDP-bound pool before its N-terminal amphipathic helix engages a membrane, so the assertion is true of all descendants. Assessed SOUND in the family review; the objection is granularity, not placement. UniProtKB:P84077 · ARF1, Homo sapiens SUPPORTS TRANSFER Canonical family member with curated cytosolic localization; supports the generic compartment claim without licensing anything more specific. FB:FBgn0035866 · Arl5, Drosophila melanogaster SUPPORTS TRANSFER The closest seed to this target -- the single-copy invertebrate ARL5 ortholog (Q9VSG8, PANTHER PTHR11711:SF31), which also seeds the ARL5-clade TGN node. Supporting Evidence: file:XENTR/F6WPT1/F6WPT1-deep-research-falcon.md The ARF family proteins are distinguished from other Ras superfamily members by their unique N-terminal amphipathic helix, which undergoes lipid modification (myristoylation or acetylation) and is critical for membrane association PMID:22245584 the dominant-negative Arl5b (T30N)-GFP mutant was dispersed throughout the cytoplasm |
| GO:0016192 vesicle-mediated transport | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic annotation of vesicle-mediated transport. ARL5A regulates endosome-to-TGN retrograde trafficking by recruiting the GARP tethering complex, which promotes SNARE-dependent fusion of endosome-derived carriers with the TGN. This is clearly a form of vesicle-mediated transport, though the term is broad. Reason: ARL5A has a well-established role in vesicle-mediated transport, specifically endosome-to-TGN retrograde trafficking mediated by GARP-dependent vesicle tethering and SNARE-dependent fusion. The IBA inference from Arf-family orthologs is well supported by experimental evidence in mammalian systems. While more specific BP terms could be used, this annotation accurately captures a core function of ARL5A. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000918181 · PAINT node asserting vesicle-mediated transport SUPPORTS TRANSFER Intermediate node above the ARL5 clade (PAINT snapshot 20260828), seeded by the classical ARFs, yeast ARL1 and Drosophila Arl5 together. The breadth of the seed set matches the breadth of the term: what these proteins share is regulation of vesicular traffic, asserted without committing to a compartment or direction. Assessed SOUND in the family review. FB:FBgn0035866 · Arl5, Drosophila melanogaster SUPPORTS TRANSFER The target's own orthology group among the seeds, which is what makes this transfer specific rather than merely family-level. UniProtKB:P84077 · ARF1, Homo sapiens SUPPORTS TRANSFER Golgi-branch seed; supports the parent term but not the retrograde route specifically, which is why the specific biology is carried in core_functions rather than by proposing a narrower replacement here. Supporting Evidence: file:XENTR/F6WPT1/F6WPT1-deep-research-falcon.md The primary and best-characterized function of ARL5 is regulation of retrograde membrane trafficking from endosomes to the TGN PMID:25795912 we find that Arl5 interacts with the Golgi-associated retrograde protein (GARP) complex that acts in the tethering of vesicles moving from endosomes to the trans-Golgi network (TGN) PMID:22245584 Arl5b is a TGN-localised small G protein that plays a key role in regulating transport along the endosome-TGN pathway |
| GO:0006886 intracellular protein transport | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic annotation of intracellular protein transport. ARL5A mediates retrograde transport of cargo proteins (TGN46, mannose-6-phosphate receptors, furin, sortilin) from endosomes back to the TGN. This is a form of intracellular protein transport, though the term is broad. Reason: ARL5A is directly involved in intracellular protein transport -- specifically, the retrograde transport of TGN-resident membrane proteins from endosomes back to the TGN. Loss of ARL5 causes mislocalization and endosomal accumulation of these cargo proteins. The IBA annotation is consistent with the known function from mammalian orthologs. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000918181 · PAINT node asserting intracellular protein transport SUPPORTS TRANSFER Same intermediate node as the vesicle-mediated transport row (PAINT snapshot 20250902), here with a seed set spanning the ciliary branch (mouse Arl6) as well as the Golgi and TGN branches. That mixture is why PAINT asserted the generic parent rather than a compartment-specific child -- the curator placed what the seeds actually share. Assessed SOUND in the family review. MGI:MGI:1927136 · Arl6, Mus musculus SUPPORTS SOURCE BUT NOT TARGET Verified at MGI as Arl6/BBS3, the ciliary BBSome GTPase (PANTHER PTHR11711:SF21, flagged as diverged in the family review). Its protein-transport evidence is real but ciliary; it supports the generic parent term only, and nothing narrower should be read across from it to an ARL5-clade member. SGD:S000000368 · ARL1, Saccharomyces cerevisiae SUPPORTS TRANSFER TGN-acting Arf-like GTPase; the seed closest in compartment to the target, though it tethers golgins rather than GARP. WB:WBGene00000182 · arf-1, Caenorhabditis elegans SUPPORTS TRANSFER Classical-ARF branch seed supporting the parent term. Supporting Evidence: file:XENTR/F6WPT1/F6WPT1-deep-research-falcon.md This pathway is essential for recycling TGN-resident membrane proteins, including TGN46, cation-independent mannose-6-phosphate receptor (CI-MPR), cation-dependent MPR (CD-MPR), furin, and sortilin, which cycle between the TGN, plasma membrane, and endosomes PMID:22245584 Depletion of Arl5b by RNAi resulted in an alteration in the intracellular distribution of mannose-6-phosphate receptor, and significantly reduced the endosome-to-TGN transport of the membrane cargo TGN38 and of Shiga toxin PMID:31575603 We also show that this mechanism is essential for the delivery of retrograde cargos to the TGN |
| GO:0005525 GTP binding | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic annotation of GTP binding. ARL5A is a small GTPase that cycles between GDP-bound and GTP-bound states. GTP binding is an inherent property of all ARF-family GTPases and is essential for ARL5A function, as the GTP-bound form recruits effectors GARP, ARMH3, and PI4KB. The UniProt entry includes a GTP-binding site at residues 23-30, 69, and 125-128. Reason: GTP binding is a fundamental and well-established molecular function of ARL5A as a member of the ARF-family small GTPases. The protein contains conserved GTP-binding motifs (P-loop, switch regions) confirmed by domain analysis. Mutant studies (constitutively active Q70L and dominant-negative T30N) confirm the GTP-binding cycle is essential for function. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000917851 · PAINT node asserting GTP binding across the Arf/Arl family SUPPORTS TRANSFER Deep node (PAINT snapshot 20230110) asserting the property that defines the family. Assessed SOUND in the family review: no PTHR11711 subfamily was found with a degenerate nucleotide site, so a deep placement is correct rather than over-broad, and the family review scopes the term FAMILY_WIDE. UniProtKB:P62330 · ARF6, Homo sapiens SUPPORTS TRANSFER Plasma-membrane-branch seed. Its compartment differs from the target's, which is irrelevant here -- the transferred property is the nucleotide site, which is shared. FB:FBgn0000115 · Arl1, Drosophila melanogaster SUPPORTS TRANSFER Arf-like branch seed with the same G domain architecture. Supporting Evidence: file:XENTR/F6WPT1/F6WPT1-deep-research-falcon.md ARL5A functions as a molecular switch that cycles between an inactive GDP-bound state and an active GTP-bound state file:XENTR/F6WPT1/F6WPT1-uniprot.txt Belongs to the small GTPase superfamily. Arf family. PMID:22245584 The constitutively active Arl5b (Q70L)-GFP mutant was localised efficiently to the Golgi in HeLa cells whereas the dominant-negative Arl5b (T30N)-GFP mutant was dispersed throughout the cytoplasm and resulted in perturbation of the Golgi apparatus PMID:31575603 Like other small GTPases, ARL5 and ARFRP1 cycle between GTP-bound, active and GDP-bound, inactive forms |
| GO:0005802 trans-Golgi network | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic annotation of trans-Golgi network localization. The TGN is the primary site of ARL5A function. In mammalian cells, ARL5A colocalizes strongly with the TGN marker TGN46 rather than with cis- or medial-Golgi markers. TGN localization is dependent on the upstream ARFRP1-SYS1 complex, and it is at the TGN that ARL5A recruits its major effectors GARP, ARMH3, and PI4KB. Reason: Trans-Golgi network localization is the primary and best-characterized subcellular location for ARL5A function. Immunofluorescence and live-cell imaging in mammalian systems demonstrate strong TGN enrichment, and genetic studies show TGN localization depends on the upstream ARFRP1-SYS1 complex. This is a core localization annotation. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000195484 · PAINT node placing trans-Golgi network at the ARL5 clade SUPPORTS TRANSFER The decisive source, and the reason this row is core rather than generic. This is the ARL5-clade node (PAINT snapshot 20171006, taxon Eukaryota), not the family root: the family's other compartment assertions sit at separate nodes (plasma membrane at PTN000918064 and PTN002619726, Golgi apparatus at PTN000195580, lysosomal membrane at PTN000918220, axoneme at PTN000196179), so TGN does not descend to ARF6 or ARL6/BBS3. The family review scopes GO:0005802 SUBFAMILY_ONLY to the three ARL5 subfamilies and assesses this node SOUND. FB:FBgn0035866 · Arl5, Drosophila melanogaster SUPPORTS TRANSFER The node's only declared seed for this term, resolved at FlyBase and UniProt as Drosophila Arl5 (Q9VSG8, PANTHER PTHR11711:SF31) -- the single-copy invertebrate ortholog of this gene, not a distant paralog. A one-seed with-list is not weak support: the curator's claim is about where TGN localization arose, and the sibling assertion at the same node is additionally seeded by human ARL5A and ARL5B, which are likewise TGN-localized downstream of ARFRP1-SYS1. Supporting Evidence: file:XENTR/F6WPT1/F6WPT1-deep-research-falcon.md ARL5A is predominantly localized to the TGN, where it colocalizes strongly with the TGN marker TGN46 rather than with cis- or medial-Golgi markers PMID:22245584 Here we show that Arl5a and Arl5b are localised to the trans-Golgi in mammalian cells PMID:39580461 ARL5 is a member of the ARF family of small GTPases that is recruited to the trans-Golgi network (TGN) by another ARF-family member, ARFRP1, in complex with the transmembrane protein SYS1 |
| GO:1903292 protein localization to Golgi membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic annotation of involvement in protein localization to Golgi membrane. ARL5A promotes retrograde transport of cargo proteins from endosomes to the TGN via GARP recruitment, which effectively maintains the steady-state localization of TGN-resident membrane proteins at the Golgi. Loss of ARL5 causes displacement of proteins such as TGN46 from the Golgi, consistent with a role in protein localization to Golgi membrane. Reason: ARL5A-dependent retrograde trafficking is essential for maintaining the localization of TGN-resident proteins at the Golgi. When ARL5 is depleted, cargo proteins accumulate in endosomes rather than at the TGN. The IBA annotation accurately reflects this role. This is a downstream consequence of GARP-mediated retrograde transport. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000195484 · PAINT node placing protein localization to Golgi membrane at the ARL5 clade SUPPORTS TRANSFER The ARL5-clade node again (PAINT snapshot 20171006), here seeded by all three characterized ARL5 orthologs. Assessed SOUND in the family review. The family review leaves this term's family-level scope UNRESOLVED -- it is also grounded independently by direct experiment on human ARF1 in a distant branch, so no closed subfamily list can be asserted across 77 subfamilies -- but the node placement is what governs the transfer to this gene, and it is sound. UniProtKB:Q9Y689 · ARL5A, Homo sapiens SUPPORTS TRANSFER The direct vertebrate ortholog of this gene and the anchor of the family's g_domain site. Its GARP-recruitment phenotype -- TGN-resident cargo stranded in endosomes when ARL5 is lost -- is the experimental basis for the asserted term. UniProtKB:Q96KC2 · ARL5B, Homo sapiens SUPPORTS TRANSFER The vertebrate paralog, largely redundant with ARL5A; most retrograde phenotypes require depleting both, which is why both seed the node. Supporting Evidence: file:XENTR/F6WPT1/F6WPT1-deep-research-falcon.md Depletion of ARL5 (or its paralogs ARL5A/5B together) significantly impairs retrograde trafficking, leading to mislocalization and accumulation of cargo proteins in endosomal compartments PMID:25795912 In Drosophila tissues the GARP complex is partially displaced from the Golgi when Arl5 is absent, and the late endosomal compartment is enlarged. In addition, in HeLa cells GARP also becomes cytosolic upon depletion of Arl5b. PMID:31575603 we observed that KO of ARL5 or ARFRP1 caused dispersal of TGN46 from the TGN similar to that caused by VPS54 KO |
| GO:0003924 GTPase activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based annotation of GTPase activity derived from the ARF/SAR family domain (IPR006689). ARL5A is a small GTPase that hydrolyzes GTP to GDP plus inorganic phosphate. The GTPase cycle (GTP-bound active to GDP-bound inactive) is the core molecular switch mechanism that controls ARL5A effector recruitment and membrane trafficking function. Reason: GTPase activity is a core molecular function of ARL5A. As an ARF-family GTPase, the protein hydrolyzes GTP as part of its regulatory cycle. The InterPro domain assignment (IPR006689, Small_GTPase_ARF/SAR) is correct, and the P-loop NTPase fold with conserved catalytic residues supports GTPase activity. This is distinct from but complementary to the GTP binding annotation -- together they describe the complete GTPase cycle. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR006689 · Small GTPase, ARF/SAR type SUPPORTS TRANSFER Domain-based rather than phylogenetic propagation (GO_REF:0000002), recorded here alongside the IBA rows because it is the same kind of inference and rests on the same evidence: the target matches the ARF/SAR G-domain signature and retains every curated nucleotide-binding and switch position. The family review leaves GO:0003924 UNRESOLVED at family level (hydrolysis is GAP-assisted and divergent branches were not inventoried), which does not weaken this target-level acceptance: it rests on the target's own verified g_domain residues and the characterized activity of its ARL5 orthologs. Supporting Evidence: file:XENTR/F6WPT1/F6WPT1-deep-research-falcon.md The primary enzymatic activity is GTP hydrolysis, converting GTP to GDP plus inorganic phosphate PMID:31575603 Like other small GTPases, ARL5 and ARFRP1 cycle between GTP-bound, active and GDP-bound, inactive forms PMID:30478271 Ragulator might function as a guanine nucleotide exchange factor to activate Arl5 |
| GO:0005525 GTP binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based annotation of GTP binding derived from multiple domain hits (IPR005225 Small_GTP-bd, IPR006689 Small_GTPase_ARF/SAR, IPR024156 Small_GTPase_ARF). This annotation is redundant with the IBA annotation for the same term (GO:0005525) but derives from a different evidence source. The GTP-binding site residues are annotated in the UniProt entry at positions 23-30, 69, and 125-128. Reason: GTP binding is a fundamental function of ARL5A confirmed by multiple independent domain annotations. While redundant with the IBA annotation for the same GO term, the InterPro evidence provides independent computational support. The domain architecture (Arf domain, P-loop NTPase fold) is fully consistent with GTP binding activity. Supporting Evidence: file:XENTR/F6WPT1/F6WPT1-deep-research-falcon.md ARL5A binds and hydrolyzes GTP; in the GTP-bound state it recruits effectors to specific membranes rather than catalyzing chemistry on a small-molecule substrate PMID:39580461 we found that the armadillo-repeat protein ARMH3 (C10orf76) binds to active, but not inactive, ARL5 |
| GO:1903292 protein localization to Golgi membrane | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine learning prediction of involvement in protein localization to Golgi membrane. This is redundant with the IBA annotation for the same term (GO:1903292) but derives from an independent computational method. ARL5A promotes retrograde transport from endosomes to the TGN, maintaining steady-state localization of TGN-resident proteins at the Golgi membrane. Reason: The ARBA prediction is consistent with established ARL5A function in retrograde trafficking to the TGN. While redundant with the IBA annotation, the ARBA prediction provides independent computational support. The biological role in maintaining Golgi membrane protein localization through GARP-dependent retrograde trafficking is well-established in mammalian systems. Supporting Evidence: file:XENTR/F6WPT1/F6WPT1-deep-research-falcon.md ARL5 recruits GARP to the TGN, where GARP functions as a tethering factor to promote SNARE-dependent fusion of endosome-derived retrograde transport carriers with the TGN membrane PMID:39580461 We observed that ARL5-KO and VPS54-KO HeLa cells exhibited reduced TGN46 localization to the TGN PMID:25795912 Thus it appears that Arl5 is one of the factors that directs the recruitment of the GARP complex to the trans-Golgi, and this function is conserved in both flies and humans |
| GO:0042147 retrograde transport, endosome to Golgi | ISS PMID:25795912 The small G protein Arl5 contributes to endosome-to-Golgi tr... | NEW | Summary: Endosome-to-Golgi retrograde transport is the specific biological process that the cached primary literature establishes for ARL5 proteins: ARL5 recruits the GARP tethering complex to the trans-Golgi, and loss of ARL5 impairs delivery of retrograde cargo (TGN46, Shiga toxin B subunit, mannose-6-phosphate receptors) from endosomes to the TGN. The existing broad IBA terms (GO:0016192, GO:0006886) are true but blur exactly this function. Reason: Proposed as the specific BP term for the process the accepted broad IBA terms under-call. Support is orthology-based (mammalian ARL5A/ARL5B and Drosophila Arl5 experiments; no Xenopus tropicalis-specific functional data exist), hence ISS rather than an experimental code. The term is directly supported by three independent cached primary papers. Supporting Evidence: PMID:25795912 Thus it appears that Arl5 is one of the factors that directs the recruitment of the GARP complex to the trans-Golgi, and this function is conserved in both flies and humans PMID:31575603 Altered localization of TGN46 and impaired transport of STxB to the Golgi complex in ARL5-KO and ARFRP1-KO cells PMID:22245584 Depletion of Arl5b by RNAi resulted in an alteration in the intracellular distribution of mannose-6-phosphate receptor, and significantly reduced the endosome-to-TGN transport of the membrane cargo TGN38 and of Shiga toxin |
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Download this section (compressed HTML)These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
View prediction review YAML · F6WPT1-protnlm-predictions-review.yaml · Review status: COMPLETE
ProtNLM2 made no predictions (GO or subcellular location) for ADP-ribosylation factor-like protein 1. The model returned only a protein name.
Source documents: genes/XENTR/F6WPT1/F6WPT1-uniprot.txt · genes/XENTR/F6WPT1/F6WPT1-goa.tsv
No GO/EC predictions in the reviewed source.
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