arl5a encodes ADP-ribosylation factor-like protein 5A, a 179-residue small GTPase of the ARF family (Ras superfamily) that retains a complete G domain (P-loop GLDNAGKT, switch II WDIGGQ, G4 NKQD). It is the Xenopus member of the vertebrate ARL5A subfamily, the same subfamily as human ARL5A, and its paralog ARL5B arose in the vertebrate duplication of a single ancestral ARL5. ARL5 proteins act as molecular switches at the trans-Golgi network (TGN): they are recruited there by the GTPase ARFRP1 bound to the membrane protein SYS1, and in the GTP-bound state they recruit the GARP tethering complex (VPS51/52/53/54), which captures endosome-derived carriers so that TGN-resident proteins such as TGN46 and mannose-6-phosphate receptors are returned from endosomes to the TGN. GTP-bound ARL5A and ARL5B also bind ARMH3, which activates phosphatidylinositol 4-kinase beta (PI4KB) to make the main TGN pool of phosphatidylinositol 4-phosphate. In mammalian cells ARL5A and ARL5B are partly redundant, and the clearest retrograde and Ragulator (LAMTOR1)-binding phenotypes were measured on ARL5B or on combined depletion. No Xenopus tropicalis functional studies exist; these roles are inferred from the mammalian and Drosophila ARL5 orthologs.
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 true -- ARL5A is a peripheral membrane protein and the trans-Golgi network is part of the cytoplasm -- but the qualifier is is_active_in, and the place where ARL5 is active (GTP-bound, effector-engaged) is the trans-Golgi network, not the cytoplasm at large. Re-review 2026-10-21: the earlier KEEP_AS_NON_CORE argued that the term was too broad, which by project rule calls for MODIFY. The replacement GO:0005802 is a part_of descendant of cytoplasm that this gene already carries by IBA from the ARL5-clade node PTN000195484.
Propagation Review
Root cause:TERM SCOPING PROBLEM
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.
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
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: True but too general. The vesicle-mediated transport that ARL5 proteins take part in is specifically endosome-to-TGN retrograde transport, through recruitment of the GARP tether that captures endosome-derived carriers. GO:0042147 retrograde transport, endosome to Golgi is an is_a descendant of GO:0016192 (verified via OLS4 hierarchicalAncestors) and is proposed for this gene as a NEW row below; FlyBase curators made the same specific annotation by IMP to the fly ortholog Arl5 from PMID:25795912. Re-review 2026-10-21: changed from ACCEPT, because the earlier reason itself conceded that a more specific term applies. The node assertion (PTN000918181) is sound at its own breadth; only the term is too coarse for this target.
Propagation Review
Root cause:TERM SCOPING PROBLEM
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.
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)
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: The cargo that ARL5-dependent retrograde traffic returns to the TGN consists of membrane proteins (TGN46/TGN38, mannose-6-phosphate receptors), and loss of ARL5 strands them in endosomes, so the term is true. GO has no descendant of intracellular protein transport that names the endosome-to-TGN route (the specific route term GO:0042147 sits under vesicle-mediated transport and endosomal transport, not under GO:0006886), so the term is as precise as this branch allows and MODIFY is not available. Re-review 2026-10-21: changed from ACCEPT to KEEP_AS_NON_CORE, since the gene's process is captured by GO:0042147, and this row describes cargo class rather than ARL5's own step. The node seed set includes ciliary Arl6, which is why PAINT asserted the generic parent.
Propagation Review
Root cause:NO FAILURE NON 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
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
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.
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
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
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
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. Re-review 2026-10-21: the stronger reading of this term is the direct one. GTP-bound ARL5 is itself the membrane receptor that localizes the GARP complex and ARMH3 to the trans-Golgi membrane (GARP becomes cytosolic when ARL5 is lost), which is protein localization to Golgi membrane carried out by ARL5. This is also the term that experimental curators chose for human ARL5B from PMID:25795912 and that PAINT placed at the ARL5-clade node PTN000195484 with fly Arl5, human ARL5A and ARL5B as seeds. F6WPT1 is in PTHR11711:SF147, the vertebrate ARL5A subfamily inside that clade.
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
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.
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
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
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 and with GTP-bound ARL5 recruiting GARP and ARMH3 to the TGN membrane. It agrees with the IBA row for the same term and is accepted for consistency with it; the support is the ARL5 ortholog literature, not the ARBA rule itself. 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
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 broad IBA terms under-call (the replacement for the GO:0016192 MODIFY). Support is orthology-based, hence ISS: F6WPT1 is PTHR11711:SF147 (vertebrate ARL5A, the subfamily of human ARL5A) inside the ARL5 clade (PTN000195484), and no Xenopus functional data exist. Participation test: ARL5 does part of the work of this process, not merely being required for it, because GTP-bound ARL5 is the TGN receptor that recruits the GARP tether which captures the incoming endosome-derived carriers. Comparator check: FlyBase gives the single-copy fly ortholog Arl5 GO:0042147 by IMP (PMID:25795912), so curators do use this term for an ARL5. Re-review 2026-10-21, on the PAINT omission: the ARL5-clade node propagated GO:1903292 and GO:0005802 but not GO:0042147. That choice was made in the 20171006 snapshot, before the human knockout data (PMID:31575603, 2019: ARL5A/ARL5B double KO abolishes GARP at the TGN and impairs Shiga toxin B delivery to the Golgi). The vertebrate cargo-transport evidence is therefore newer than the PAINT decision, which is why this row departs from it; a reviewer who prefers to defer to the node can treat GO:1903292 as the clade-level statement of the same mechanism. Caveat: single-paralog knockdown data are for ARL5B (Houghton 2012), and the knockout data are for ARL5A plus ARL5B together.
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
double KO of ARL5A and ARL5B (hereafter referred to as ARL5 KO), but not ARL1 or double KO of RAB6A and RAB6B (referred to as RAB6 KO), abrogated the association of GARP with the TGN
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
Core Functions
GTP-regulated molecular switch at the trans-Golgi network. ARL5A is brought to the TGN by ARFRP1-SYS1 and, when GTP-bound, recruits the GARP tethering complex to the TGN membrane, so that endosome-derived carriers bearing TGN-resident membrane proteins (TGN46/TGN38, mannose-6-phosphate receptors) are captured and fused with the TGN. GTP-bound ARL5 also recruits ARMH3, which activates PI4KB to make TGN PI4P (a second effector branch, not required for cargo retrieval). A Ragulator (LAMTOR1) interaction linking amino acid availability to this traffic has been shown mainly for the paralog ARL5B; ARL5A binds LAMTOR1 in pulldowns, but its contribution is less clear. Inferred for Xenopus arl5a (PTHR11711:SF147, vertebrate ARL5A subfamily) from mammalian and Drosophila ARL5 orthologs; there are no Xenopus functional data.
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)
Herein we report that the ARF-like (ARL) GTPase ARFRP1 functions upstream of two other ARL GTPases, ARL1 and ARL5, which in turn recruit golgins and GARP, respectively, to the TGN
ARMH3 functions to activate phosphatidylinositol 4-kinase IIIβ (PI4KB), accounting for the main pool of phosphatidylinositol 4-phosphate (PI4P) at the TGN
Arl5, an ARF-like family small GTPase, interacts with Ragulator in an AA-regulated manner and both Arl5 and its effector, the Golgi-associated retrograde protein complex (GARP), are required for the AA-stimulated trafficking ... we demonstrate that SLC38A9, v-ATPase and Ragulator, but not Rag GTPases and mTORC1, are essential for the AA-stimulated trafficking
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.
ProtNLM2 made no GO or subcellular-location predictions for F6WPT1, the Xenopus tropicalis arl5a gene product (ADP-ribosylation factor-like protein 5A, a trans-Golgi network ARF-family GTPase of the vertebrate ARL5A subfamily). The model returned only a protein name, "ADP-ribosylation factor-like protein 1", which places the protein in the ARF-like family but names the wrong paralog (ARL1 rather than ARL5A). No GO term is predicted, so there is nothing to score; this file records an assessed absence of GO output. The gene's supported functions (GTP binding, GTPase activity, trans-Golgi network localization, protein localization to Golgi membrane, vesicle-mediated transport and intracellular protein transport) come from its GOA annotations and the ARL5 phylogenetic node, not from ProtNLM2.