ARL3 (P36405) research notes

ADP-ribosylation factor-like protein 3, human. Small Arf-family GTPase; cargo-release factor for lipidated ciliary proteins.

Deep research status

The first falcon run timed out at the 600 s default (the perplexity-lite fallback is unavailable). The rerun with --timeout 2400 was reported as timed out, but the falcon job eventually completed and wrote ARL3-deep-research-falcon.md at 22:29, after the initial review. I then read it and checked it against the review. It changes no actions:
- It supports the switch/release-factor framing (G protein activity rather than GTPase activity as the core MF): ["The best-supported functional annotation remains: a GTP-dependent, spatially regulated allosteric release factor ... with ARL13B/BART-dependent activation and RP2-dependent termination"] and ["ARL3-GTP binds these carriers allosterically and promotes cargo release at the cilium; it is neither the lipid-modifying enzyme nor the cargo’s membrane transporter."]
- It supports removing the NOT cilium row: ["ARL3 is a soluble, cilia-associated protein that can occur in the cell body as well as the ciliary compartment."]
- It supports marking small GTPase-mediated signal transduction as over-annotated: ["Ciliary signaling is chiefly a consequence of cargo composition, not a demonstrated direct receptor pathway for ARL3."]
- Correction: early retina-wide Arl3 deletion in mouse prevents connecting cilium and outer segment formation (Hanke-Gogokhia 2016, via the deep research). The cilium assembly reasons were reworded, since cilia are not universally independent of ARL3; both rows stay KEEP_AS_NON_CORE.
- New items not annotated: BART/ARL2BP acts as a co-GEF with ARL13B (ElMaghloob 2021). ARL3-GTP displaces DNAAF9/Shulin from outer dynein arms (2024 preprint, 2025 NSMB). Neither is cached here, so no new annotations were made.

Summary of function

• Nucleotide binding with unusual biochemistry. PMID:8034651
• GAP is RP2. [PMID:18588884 "Recently, we could identify RP2, responsible for a variant of X-linked retinitis pigmentosa, as the Arl3-specific GAP."; PMID:11847227 "Finally, we find that RP2 interacts with GTP-bound ADP ribosylation factor-like 3 protein"]
• GEF is ARL13B; Joubert variants at Arg149. PMID:30269812
• Cargo release: [PMID:22085962 "Furthermore, we found that binding of ARL3-GTP serves to release myristoylated cargo from UNC119."; "Our results uncover a selective, membrane targeting GTPase cycle that delivers myristoylated proteins to the ciliary membrane"]; PMID:26455799; PMID:22002721
• Other locations and roles: centrosomes, spindles, midbodies, cilia, Golgi, nucleoplasm. Knockdown causes cytokinesis failure. PMID:16525022 Photoreceptor connecting cilium PMID:12417528

Key curation decisions

• Core MF: G protein activity (GO:0003925), which covers small GTPase switches. GTPase activity (IEA) is accepted but is RP2-dependent. GTP-dependent protein binding (GO:0030742; verified in OLS) is used as the replacement for effector protein-binding rows (PDE6D, UNC119, ARL2BP). GTPase activating protein binding (GO:0032794) replaces the RP2 row. TBL1X and Q5TEA3 rows REMOVE.
• NOT cilium (IDA, PMID:17646400) REMOVE. It is contradicted by endogenous (PMID:16525022, PMID:12417528), HPA and functional (PMID:30269812) evidence, and the cached text mentions Arl3 only by analogy.
• Small GTPase-mediated signal transduction (IDA, PMID:22085962): MARK_AS_OVER_ANNOTATED. The paper describes a protein-targeting GTPase cycle, not signal transduction.
• Cilium assembly (IBA, IMP zebrafish): KEEP_AS_NON_CORE. Patient fibroblasts form normal cilia, but early Arl3 deletion blocks photoreceptor ciliogenesis in mouse (per the deep research); the core defect is in membrane composition.
• Cytokinesis, midbody, spindle, Golgi, nucleus and microtubule binding: KEEP_AS_NON_CORE.

HPA cilium atlas vs module role

• Module stage 5 (ciliary_membrane_composition): "ARL3-GTP displaces lipidated cargo from PDE6D and UNC119B inside the cilium". Module MF GO:0003924 GTPase activity; process protein localization to cilium.
• HPA v25: Primary cilium (Supported), Basal body (Approved), Centrosome (Supported); main locations Basal body, Centrosome and Nucleoplasm. GOA HPA rows: cilium (ACCEPT), centrosome and nucleoplasm (non-core).
• Assessment: HPA supports the module's ciliary placement. One difference in MF choice: I use G protein activity (GO:0003925) rather than the module's GTPase activity (GO:0003924) as the core MF. ARL3's intrinsic GTP hydrolysis is negligible and GAP (RP2)-driven, and its function is the GTP-dependent effector binding that releases cargo, which is the switch function GO:0003925 describes. Hydrolysis by RP2 is the off-step (inactivation), not the cargo-release step. The process (protein localization to cilium / ciliary membrane) agrees with the module.