{"gene":"ARL16","run_date":"2026-04-28T17:12:37","timeline":{"discoveries":[{"year":2011,"finding":"ARL16 binds directly to the C-terminal domain (CTD) of RIG-I in a GTP-dependent manner, suppressing the association between RIG-I and RNA, thereby inhibiting RIG-I-mediated downstream signaling and antiviral activity. A GDP-locked mutant (T37N) and a deletion mutant (Δ45-54) abolished both RIG-I binding and inhibitory function.","method":"Co-immunoprecipitation, overexpression/knockdown with IFN-β reporter assay, domain mapping, GTP-binding mutant analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, domain-specific mutants, RNAi knockdown with functional readout, multiple orthogonal methods in single study","pmids":["21233210"],"is_preprint":false},{"year":2022,"finding":"ARL16 is required for ciliogenesis and ciliary protein trafficking; deletion of Arl16 in mouse embryonic fibroblasts decreases ciliogenesis but increases ciliary length, causes loss of ARL13B, ARL3, INPP5E, and IFT140 from cilia, and leads to accumulation of INPP5E and IFT140 at the Golgi, indicating ARL16 regulates a specific Golgi-to-cilia traffic pathway for IFT140 and INPP5E.","method":"CRISPR/Cas9 knockout in MEFs, immunofluorescence microscopy, subcellular fractionation/localization, ciliary length measurement","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined cellular phenotype and specific cargo localization, multiple orthogonal readouts","pmids":["35196065"],"is_preprint":false},{"year":2021,"finding":"Expression of activating (GTP-locked) mutants of ARL16 rescues the ciliogenesis and ciliary protein trafficking defects caused by deletion of ELMOD1 or ELMOD3 (ARF GAPs), placing ARL16 downstream of or in the same pathway as ELMOD1/3 in Golgi-to-cilia traffic.","method":"Genetic epistasis — activating mutant rescue of ELMOD1/3 KO phenotypes in MEFs","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 — epistasis by activating mutant rescue, but ARL16 is not the primary subject of the paper","pmids":["34818063"],"is_preprint":false},{"year":2021,"finding":"Phylogenetic analysis across 114 eukaryotic species establishes that ARL16 is ancient, present in the last eukaryotic common ancestor, and belongs to the ARF GTPase family.","method":"Comprehensive molecular phylogenetic analysis of >2,000 manually curated ARF family genes","journal":"Genome biology and evolution","confidence":"Medium","confidence_rationale":"Tier 2 — large-scale phylogenomics with manual curation, but purely evolutionary/no direct functional experiment","pmids":["34247240"],"is_preprint":false}],"current_model":"ARL16 is an ancient ARF-family GTPase that acts in GTP-bound form to inhibit innate immune signaling by binding the C-terminal domain of RIG-I and blocking its RNA association, and also functions at the Golgi to regulate a specific trafficking pathway required for export of IFT140 and INPP5E to cilia, placing it downstream of the ARF GAPs ELMOD1/3 in Golgi-to-cilia traffic."},"narrative":{"teleology":[{"year":2011,"claim":"The first functional role for ARL16 was established as a GTP-dependent negative regulator of innate immunity, resolving how a small GTPase could directly modulate RIG-I signaling by competing with RNA binding at RIG-I's C-terminal domain.","evidence":"Co-immunoprecipitation with domain-mapping and GTP-binding mutants, RNAi knockdown with IFN-β reporter assays in cultured cells","pmids":["21233210"],"confidence":"High","gaps":["Endogenous stoichiometry and physiological conditions under which ARL16 inhibits RIG-I are not defined","No GAP or GEF identified for ARL16 in the RIG-I context","Whether ARL16's immune and ciliary functions are coordinated or independent is unknown"]},{"year":2021,"claim":"Phylogenetic analysis established ARL16 as an ancient member of the ARF GTPase family present in the last eukaryotic common ancestor, suggesting deeply conserved functions beyond mammalian immunity.","evidence":"Molecular phylogenetics across 114 eukaryotic species with manual curation of >2,000 ARF family sequences","pmids":["34247240"],"confidence":"Medium","gaps":["No functional data accompany the phylogenetic assignment","Whether ancestral ARL16 function relates to cilia or immunity is unresolved"]},{"year":2022,"claim":"ARL16 was shown to operate at the Golgi in a specific trafficking pathway required for ciliary delivery of IFT140 and INPP5E, and epistasis experiments placed it downstream of the ARF GAPs ELMOD1/3, establishing a second major cellular role for this GTPase.","evidence":"CRISPR/Cas9 knockout in MEFs with immunofluorescence, subcellular fractionation, ciliary measurements; GTP-locked ARL16 mutant rescue of ELMOD1/3 KO phenotypes","pmids":["35196065","34818063"],"confidence":"High","gaps":["Direct effectors of ARL16 at the Golgi are unknown","How ARL16 activation is regulated by ELMOD1/3 (direct substrate vs. indirect) is not resolved","Mechanism by which ARL16 loss increases ciliary length while reducing ciliogenesis is unexplained"]},{"year":null,"claim":"No GEF or GAP specific to ARL16 has been biochemically identified, no structural model of ARL16 in complex with any partner exists, and whether the immune-regulatory and ciliary trafficking functions involve shared or distinct pools of ARL16 remains open.","evidence":"","pmids":[],"confidence":"Low","gaps":["No GEF identified for ARL16","No crystal or cryo-EM structure available","In vivo phenotyping in whole organisms (mouse knockout) has not been reported"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[0,2]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[1]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[1]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[1,2]}],"complexes":[],"partners":["DDX58","ELMOD1","ELMOD3"],"other_free_text":[]},"mechanistic_narrative":"ARL16 is an ancient ARF-family GTPase that functions in two distinct cellular contexts: innate immune regulation and ciliary trafficking [PMID:34247240]. In its GTP-bound form, ARL16 binds directly to the C-terminal domain of the cytosolic RNA sensor RIG-I, blocking RIG-I–RNA association and thereby suppressing IFN-β signaling and antiviral responses [PMID:21233210]. At the Golgi, ARL16 is required for a specific trafficking pathway that delivers IFT140 and INPP5E to cilia; its deletion causes accumulation of these cargoes at the Golgi, reduces ciliogenesis, and depletes ARL13B and ARL3 from cilia, and GTP-locked ARL16 rescues equivalent defects caused by loss of the ARF GAPs ELMOD1/3, placing ARL16 downstream of these regulators [PMID:35196065, PMID:34818063]."},"prefetch_data":{"uniprot":{"accession":"Q0P5N6","full_name":"ADP-ribosylation factor-like protein 16","aliases":[],"length_aa":173,"mass_kda":18.6,"function":"Required for the trafficking of ciliary proteins IFT140 and INPP5E from the Golgi to the cilia, thus playing a role in ciliogenesis (By similarity). Suppresses the RNA sensing activity of RIGI in a GTP-dependent manner (PubMed:21233210)","subcellular_location":"Cytoplasm; Cytoplasm, cytoskeleton, cilium axoneme; Mitochondrion; Cytoplasm, cytoskeleton, cilium basal body; Photoreceptor inner segment","url":"https://www.uniprot.org/uniprotkb/Q0P5N6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ARL16","classification":"Not Classified","n_dependent_lines":11,"n_total_lines":383,"dependency_fraction":0.028720626631853787},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ARL16","total_profiled":1310},"omim":[{"mim_id":"619117","title":"ADP-RIBOSYLATION FACTOR-LIKE GTPase 16; ARL16","url":"https://www.omim.org/entry/619117"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Primary cilium","reliability":"Approved"},{"location":"Basal body","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ARL16"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q0P5N6","domains":[{"cath_id":"3.40.50.300","chopping":"26-196","consensus_level":"high","plddt":93.2446,"start":26,"end":196}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q0P5N6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q0P5N6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q0P5N6-F1-predicted_aligned_error_v6.png","plddt_mean":86.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ARL16","jax_strain_url":"https://www.jax.org/strain/search?query=ARL16"},"sequence":{"accession":"Q0P5N6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q0P5N6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q0P5N6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q0P5N6"}},"corpus_meta":[{"pmid":"34247240","id":"PMC_34247240","title":"A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family.","date":"2021","source":"Genome biology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/34247240","citation_count":28,"is_preprint":false},{"pmid":"21233210","id":"PMC_21233210","title":"ARF-like protein 16 (ARL16) inhibits RIG-I by binding with its C-terminal domain in a GTP-dependent manner.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21233210","citation_count":19,"is_preprint":false},{"pmid":"35196065","id":"PMC_35196065","title":"Phylogenetic profiling and cellular analyses of ARL16 reveal roles in traffic of IFT140 and INPP5E.","date":"2022","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/35196065","citation_count":13,"is_preprint":false},{"pmid":"34818063","id":"PMC_34818063","title":"The ARF GAPs ELMOD1 and ELMOD3 act at the Golgi and cilia to regulate ciliogenesis and ciliary protein traffic.","date":"2021","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/34818063","citation_count":11,"is_preprint":false},{"pmid":"36467401","id":"PMC_36467401","title":"The complex, dynamic SpliceOme of the small GTPase transcripts altered by technique, sex, genetics, tissue specificity, and RNA base editing.","date":"2022","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/36467401","citation_count":7,"is_preprint":false},{"pmid":"1686394","id":"PMC_1686394","title":"Variations in gamma-glutamyl transpeptidase glycosylation and kinetic parameters in cultured liver cells.","date":"1991","source":"Biochemistry international","url":"https://pubmed.ncbi.nlm.nih.gov/1686394","citation_count":5,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4512,"output_tokens":1036,"usd":0.014538},"stage2":{"model":"claude-opus-4-6","input_tokens":4243,"output_tokens":1365,"usd":0.08301},"total_usd":0.097548,"stage1_batch_id":"msgbatch_01TqNM6p6FsoMBT2jzQTwKBr","stage2_batch_id":"msgbatch_01Ya473eco8sTHbvRymQaU8o","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"ARL16 binds directly to the C-terminal domain (CTD) of RIG-I in a GTP-dependent manner, suppressing the association between RIG-I and RNA, thereby inhibiting RIG-I-mediated downstream signaling and antiviral activity. A GDP-locked mutant (T37N) and a deletion mutant (Δ45-54) abolished both RIG-I binding and inhibitory function.\",\n      \"method\": \"Co-immunoprecipitation, overexpression/knockdown with IFN-β reporter assay, domain mapping, GTP-binding mutant analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, domain-specific mutants, RNAi knockdown with functional readout, multiple orthogonal methods in single study\",\n      \"pmids\": [\"21233210\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ARL16 is required for ciliogenesis and ciliary protein trafficking; deletion of Arl16 in mouse embryonic fibroblasts decreases ciliogenesis but increases ciliary length, causes loss of ARL13B, ARL3, INPP5E, and IFT140 from cilia, and leads to accumulation of INPP5E and IFT140 at the Golgi, indicating ARL16 regulates a specific Golgi-to-cilia traffic pathway for IFT140 and INPP5E.\",\n      \"method\": \"CRISPR/Cas9 knockout in MEFs, immunofluorescence microscopy, subcellular fractionation/localization, ciliary length measurement\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined cellular phenotype and specific cargo localization, multiple orthogonal readouts\",\n      \"pmids\": [\"35196065\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Expression of activating (GTP-locked) mutants of ARL16 rescues the ciliogenesis and ciliary protein trafficking defects caused by deletion of ELMOD1 or ELMOD3 (ARF GAPs), placing ARL16 downstream of or in the same pathway as ELMOD1/3 in Golgi-to-cilia traffic.\",\n      \"method\": \"Genetic epistasis — activating mutant rescue of ELMOD1/3 KO phenotypes in MEFs\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epistasis by activating mutant rescue, but ARL16 is not the primary subject of the paper\",\n      \"pmids\": [\"34818063\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Phylogenetic analysis across 114 eukaryotic species establishes that ARL16 is ancient, present in the last eukaryotic common ancestor, and belongs to the ARF GTPase family.\",\n      \"method\": \"Comprehensive molecular phylogenetic analysis of >2,000 manually curated ARF family genes\",\n      \"journal\": \"Genome biology and evolution\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — large-scale phylogenomics with manual curation, but purely evolutionary/no direct functional experiment\",\n      \"pmids\": [\"34247240\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ARL16 is an ancient ARF-family GTPase that acts in GTP-bound form to inhibit innate immune signaling by binding the C-terminal domain of RIG-I and blocking its RNA association, and also functions at the Golgi to regulate a specific trafficking pathway required for export of IFT140 and INPP5E to cilia, placing it downstream of the ARF GAPs ELMOD1/3 in Golgi-to-cilia traffic.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"ARL16 is an ancient ARF-family GTPase that functions in two distinct cellular contexts: innate immune regulation and ciliary trafficking [PMID:34247240]. In its GTP-bound form, ARL16 binds directly to the C-terminal domain of the cytosolic RNA sensor RIG-I, blocking RIG-I–RNA association and thereby suppressing IFN-β signaling and antiviral responses [PMID:21233210]. At the Golgi, ARL16 is required for a specific trafficking pathway that delivers IFT140 and INPP5E to cilia; its deletion causes accumulation of these cargoes at the Golgi, reduces ciliogenesis, and depletes ARL13B and ARL3 from cilia, and GTP-locked ARL16 rescues equivalent defects caused by loss of the ARF GAPs ELMOD1/3, placing ARL16 downstream of these regulators [PMID:35196065, PMID:34818063].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"The first functional role for ARL16 was established as a GTP-dependent negative regulator of innate immunity, resolving how a small GTPase could directly modulate RIG-I signaling by competing with RNA binding at RIG-I's C-terminal domain.\",\n      \"evidence\": \"Co-immunoprecipitation with domain-mapping and GTP-binding mutants, RNAi knockdown with IFN-β reporter assays in cultured cells\",\n      \"pmids\": [\"21233210\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Endogenous stoichiometry and physiological conditions under which ARL16 inhibits RIG-I are not defined\",\n        \"No GAP or GEF identified for ARL16 in the RIG-I context\",\n        \"Whether ARL16's immune and ciliary functions are coordinated or independent is unknown\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Phylogenetic analysis established ARL16 as an ancient member of the ARF GTPase family present in the last eukaryotic common ancestor, suggesting deeply conserved functions beyond mammalian immunity.\",\n      \"evidence\": \"Molecular phylogenetics across 114 eukaryotic species with manual curation of >2,000 ARF family sequences\",\n      \"pmids\": [\"34247240\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional data accompany the phylogenetic assignment\",\n        \"Whether ancestral ARL16 function relates to cilia or immunity is unresolved\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"ARL16 was shown to operate at the Golgi in a specific trafficking pathway required for ciliary delivery of IFT140 and INPP5E, and epistasis experiments placed it downstream of the ARF GAPs ELMOD1/3, establishing a second major cellular role for this GTPase.\",\n      \"evidence\": \"CRISPR/Cas9 knockout in MEFs with immunofluorescence, subcellular fractionation, ciliary measurements; GTP-locked ARL16 mutant rescue of ELMOD1/3 KO phenotypes\",\n      \"pmids\": [\"35196065\", \"34818063\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct effectors of ARL16 at the Golgi are unknown\",\n        \"How ARL16 activation is regulated by ELMOD1/3 (direct substrate vs. indirect) is not resolved\",\n        \"Mechanism by which ARL16 loss increases ciliary length while reducing ciliogenesis is unexplained\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"No GEF or GAP specific to ARL16 has been biochemically identified, no structural model of ARL16 in complex with any partner exists, and whether the immune-regulatory and ciliary trafficking functions involve shared or distinct pools of ARL16 remains open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No GEF identified for ARL16\",\n        \"No crystal or cryo-EM structure available\",\n        \"In vivo phenotyping in whole organisms (mouse knockout) has not been reported\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"DDX58\", \"ELMOD1\", \"ELMOD3\"],\n    \"other_free_text\": []\n  }\n}\n```"}