{"gene":"ARL16","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":2011,"finding":"ARL16 inhibits RIG-I innate immune signaling by binding the C-terminal domain (CTD) of RIG-I in a GTP-dependent manner, thereby suppressing the association between RIG-I and RNA. Mutants restricted to the GDP-bound form (T37N and Δ45-54) neither bind RIG-I nor inhibit its signaling, establishing that GTP loading is required for the interaction and inhibitory function.","method":"Co-immunoprecipitation, RNA binding suppression assay, RNAi knockdown with IFN-β reporter and VSV replication readout, dominant-negative mutant analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus functional knockdown/overexpression with multiple orthogonal readouts in a single focused study","pmids":["21233210"],"is_preprint":false},{"year":2022,"finding":"ARL16 is required for ciliogenesis and for trafficking of IFT140 (an IFT-A core component) and INPP5E from the Golgi to cilia. Deletion of ARL16 in mouse embryonic fibroblasts (MEFs) decreases ciliogenesis yet 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 a specific defect in Golgi-to-cilia export of these cargoes.","method":"CRISPR/Cas9 knockout in MEFs, immunofluorescence microscopy, ciliary protein content analysis by immunostaining, Golgi accumulation assay","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean KO with defined cellular phenotype and multiple orthogonal immunofluorescence readouts in a single focused study","pmids":["35196065"],"is_preprint":false},{"year":2021,"finding":"ARL16 acts downstream of or in parallel with ELMOD1 and ELMOD3 (ARF GAPs) in a Golgi-to-cilia trafficking pathway: expression of an activating mutant of ARL16 rescues the ciliogenesis and ciliary protein-traffic defects caused by deletion of either ELMOD1 or ELMOD3, placing ARL16 in the same pathway as these GAPs.","method":"Epistasis by activating-mutant rescue in Elmod1 and Elmod3 KO MEFs, ciliogenesis assay, ciliary protein localization by immunofluorescence","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic epistasis (activating-mutant rescue) in a single lab study; ARL16 rescue is one part of a broader ELMOD1/3 paper","pmids":["34818063"],"is_preprint":false},{"year":2021,"finding":"Phylogenetic analysis across 114 eukaryotic species provides evidence that ARL16 was present in the last eukaryotic common ancestor, indicating its ancient and wide distribution in eukaryotes as a member of the ARF GTPase family.","method":"Molecular phylogenetic analysis of >2,000 manually curated ARF family genes from 114 eukaryotic species","journal":"Genome biology and evolution","confidence":"Low","confidence_rationale":"Tier 4 / Strong — computational/phylogenetic inference only; no direct biochemical or cell-biological experiment on ARL16 protein function","pmids":["34247240"],"is_preprint":false}],"current_model":"ARL16 is an ancient ARF-family GTPase that functions in two established cellular contexts: (1) in innate immunity, GTP-loaded ARL16 binds the C-terminal domain of RIG-I and blocks its association with viral RNA, thereby negatively regulating type I interferon signaling; and (2) in ciliated cells, ARL16 is required for a Golgi-to-cilia trafficking pathway that specifically exports IFT140 and INPP5E to cilia, placing it downstream of the ARF GAPs ELMOD1/3."},"narrative":{"mechanistic_narrative":"ARL16 is an ARF-family GTPase that operates as a GTP-dependent regulatory switch in two distinct cellular contexts [PMID:21233210, PMID:35196065]. In innate immunity, GTP-loaded ARL16 binds the C-terminal domain of RIG-I and suppresses RIG-I association with viral RNA, thereby negatively regulating type I interferon signaling; GDP-restricted mutants (T37N, Δ45-54) fail to bind RIG-I or inhibit its signaling, establishing that nucleotide-dependent activation is required for both the interaction and its inhibitory function [PMID:21233210]. In ciliated cells, ARL16 is required for a Golgi-to-cilia trafficking pathway that specifically exports IFT140 and INPP5E to cilia: its loss reduces ciliogenesis, depletes ARL13B, ARL3, INPP5E, and IFT140 from cilia, and causes INPP5E and IFT140 to accumulate at the Golgi [PMID:35196065]. In this pathway ARL16 acts downstream of or in parallel with the ARF GAPs ELMOD1 and ELMOD3, since an activating ARL16 mutant rescues the ciliary defects of ELMOD1 or ELMOD3 deletion [PMID:34818063]. The biochemical mechanism linking these two roles and the direct effectors of ARL16 in cilia have not been characterized in the available corpus.","teleology":[{"year":2011,"claim":"Established the first molecular function for ARL16 by showing it is a GTP-dependent negative regulator of RIG-I antiviral signaling, answering how a small GTPase restrains the interferon response.","evidence":"Co-IP, RNA-binding suppression assay, RNAi knockdown with IFN-β reporter and VSV readout, and GDP-locked dominant-negative mutants in cells","pmids":["21233210"],"confidence":"High","gaps":["Structural basis of the GTP-dependent ARL16–RIG-I CTD interaction not resolved","Upstream signals controlling ARL16 nucleotide state during infection unknown","GEF/GAP regulating ARL16 in this context not identified"]},{"year":2021,"claim":"Placed ARL16 within a defined ciliary trafficking pathway by genetic epistasis, showing it acts downstream of or in parallel with the ARF GAPs ELMOD1/3.","evidence":"Activating-mutant rescue in Elmod1 and Elmod3 KO MEFs with ciliogenesis and ciliary protein localization readouts","pmids":["34818063"],"confidence":"Medium","gaps":["Direct biochemical relationship between ELMOD1/3 GAP activity and ARL16 nucleotide cycling not demonstrated","Single-lab genetic epistasis only","Whether ELMOD1/3 act directly on ARL16 not shown"]},{"year":2021,"claim":"Phylogenetic analysis placed ARL16 in the last eukaryotic common ancestor, establishing it as an ancient and broadly conserved member of the ARF GTPase family.","evidence":"Molecular phylogenetic analysis of >2,000 curated ARF family genes across 114 eukaryotic species","pmids":["34247240"],"confidence":"Low","gaps":["Computational inference only with no experimental test of ARL16 function","Conservation of specific roles across species not addressed"]},{"year":2022,"claim":"Defined the cell-biological role of ARL16 in ciliogenesis, showing it is specifically required for Golgi-to-cilia export of IFT140 and INPP5E.","evidence":"CRISPR/Cas9 ARL16 knockout in MEFs with immunofluorescence of ciliary protein content and Golgi accumulation assays","pmids":["35196065"],"confidence":"High","gaps":["Direct effectors or cargo adaptors recruited by ARL16 not identified","Mechanism by which ARL16 selects IFT140/INPP5E cargo unknown","Increase in ciliary length despite reduced ciliogenesis unexplained"]},{"year":null,"claim":"Whether and how the immune-regulatory and ciliary-trafficking functions of ARL16 are mechanistically related, and what GEFs/GAPs and direct effectors govern its nucleotide cycle in each context, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of ARL16 in either context","Direct ciliary effectors unidentified","Regulators of ARL16 GTP loading unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[0,1,2]}],"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":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[1]}],"complexes":[],"partners":["DDX58","ELMOD1","ELMOD3"],"other_free_text":[]}},"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":29,"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":5231,"output_tokens":1177,"usd":0.016674,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7765,"output_tokens":2015,"usd":0.0446,"stage2_stop_reason":"end_turn"},"total_usd":0.061274,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"ARL16 inhibits RIG-I innate immune signaling by binding the C-terminal domain (CTD) of RIG-I in a GTP-dependent manner, thereby suppressing the association between RIG-I and RNA. Mutants restricted to the GDP-bound form (T37N and Δ45-54) neither bind RIG-I nor inhibit its signaling, establishing that GTP loading is required for the interaction and inhibitory function.\",\n      \"method\": \"Co-immunoprecipitation, RNA binding suppression assay, RNAi knockdown with IFN-β reporter and VSV replication readout, dominant-negative mutant analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus functional knockdown/overexpression with multiple orthogonal readouts in a single focused study\",\n      \"pmids\": [\"21233210\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ARL16 is required for ciliogenesis and for trafficking of IFT140 (an IFT-A core component) and INPP5E from the Golgi to cilia. Deletion of ARL16 in mouse embryonic fibroblasts (MEFs) decreases ciliogenesis yet 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 a specific defect in Golgi-to-cilia export of these cargoes.\",\n      \"method\": \"CRISPR/Cas9 knockout in MEFs, immunofluorescence microscopy, ciliary protein content analysis by immunostaining, Golgi accumulation assay\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined cellular phenotype and multiple orthogonal immunofluorescence readouts in a single focused study\",\n      \"pmids\": [\"35196065\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ARL16 acts downstream of or in parallel with ELMOD1 and ELMOD3 (ARF GAPs) in a Golgi-to-cilia trafficking pathway: expression of an activating mutant of ARL16 rescues the ciliogenesis and ciliary protein-traffic defects caused by deletion of either ELMOD1 or ELMOD3, placing ARL16 in the same pathway as these GAPs.\",\n      \"method\": \"Epistasis by activating-mutant rescue in Elmod1 and Elmod3 KO MEFs, ciliogenesis assay, ciliary protein localization by immunofluorescence\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic epistasis (activating-mutant rescue) in a single lab study; ARL16 rescue is one part of a broader ELMOD1/3 paper\",\n      \"pmids\": [\"34818063\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Phylogenetic analysis across 114 eukaryotic species provides evidence that ARL16 was present in the last eukaryotic common ancestor, indicating its ancient and wide distribution in eukaryotes as a member of the ARF GTPase family.\",\n      \"method\": \"Molecular phylogenetic analysis of >2,000 manually curated ARF family genes from 114 eukaryotic species\",\n      \"journal\": \"Genome biology and evolution\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Strong — computational/phylogenetic inference only; no direct biochemical or cell-biological experiment on ARL16 protein function\",\n      \"pmids\": [\"34247240\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ARL16 is an ancient ARF-family GTPase that functions in two established cellular contexts: (1) in innate immunity, GTP-loaded ARL16 binds the C-terminal domain of RIG-I and blocks its association with viral RNA, thereby negatively regulating type I interferon signaling; and (2) in ciliated cells, ARL16 is required for a Golgi-to-cilia trafficking pathway that specifically exports IFT140 and INPP5E to cilia, placing it downstream of the ARF GAPs ELMOD1/3.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ARL16 is an ARF-family GTPase that operates as a GTP-dependent regulatory switch in two distinct cellular contexts [#0, #1]. In innate immunity, GTP-loaded ARL16 binds the C-terminal domain of RIG-I and suppresses RIG-I association with viral RNA, thereby negatively regulating type I interferon signaling; GDP-restricted mutants (T37N, \\u039445-54) fail to bind RIG-I or inhibit its signaling, establishing that nucleotide-dependent activation is required for both the interaction and its inhibitory function [#0]. In ciliated cells, ARL16 is required for a Golgi-to-cilia trafficking pathway that specifically exports IFT140 and INPP5E to cilia: its loss reduces ciliogenesis, depletes ARL13B, ARL3, INPP5E, and IFT140 from cilia, and causes INPP5E and IFT140 to accumulate at the Golgi [#1]. In this pathway ARL16 acts downstream of or in parallel with the ARF GAPs ELMOD1 and ELMOD3, since an activating ARL16 mutant rescues the ciliary defects of ELMOD1 or ELMOD3 deletion [#2]. The biochemical mechanism linking these two roles and the direct effectors of ARL16 in cilia have not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Established the first molecular function for ARL16 by showing it is a GTP-dependent negative regulator of RIG-I antiviral signaling, answering how a small GTPase restrains the interferon response.\",\n      \"evidence\": \"Co-IP, RNA-binding suppression assay, RNAi knockdown with IFN-\\u03b2 reporter and VSV readout, and GDP-locked dominant-negative mutants in cells\",\n      \"pmids\": [\"21233210\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the GTP-dependent ARL16\\u2013RIG-I CTD interaction not resolved\", \"Upstream signals controlling ARL16 nucleotide state during infection unknown\", \"GEF/GAP regulating ARL16 in this context not identified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Placed ARL16 within a defined ciliary trafficking pathway by genetic epistasis, showing it acts downstream of or in parallel with the ARF GAPs ELMOD1/3.\",\n      \"evidence\": \"Activating-mutant rescue in Elmod1 and Elmod3 KO MEFs with ciliogenesis and ciliary protein localization readouts\",\n      \"pmids\": [\"34818063\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical relationship between ELMOD1/3 GAP activity and ARL16 nucleotide cycling not demonstrated\", \"Single-lab genetic epistasis only\", \"Whether ELMOD1/3 act directly on ARL16 not shown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Phylogenetic analysis placed ARL16 in the last eukaryotic common ancestor, establishing it as an ancient and broadly conserved member of the ARF GTPase family.\",\n      \"evidence\": \"Molecular phylogenetic analysis of >2,000 curated ARF family genes across 114 eukaryotic species\",\n      \"pmids\": [\"34247240\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Computational inference only with no experimental test of ARL16 function\", \"Conservation of specific roles across species not addressed\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined the cell-biological role of ARL16 in ciliogenesis, showing it is specifically required for Golgi-to-cilia export of IFT140 and INPP5E.\",\n      \"evidence\": \"CRISPR/Cas9 ARL16 knockout in MEFs with immunofluorescence of ciliary protein content and Golgi accumulation assays\",\n      \"pmids\": [\"35196065\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct effectors or cargo adaptors recruited by ARL16 not identified\", \"Mechanism by which ARL16 selects IFT140/INPP5E cargo unknown\", \"Increase in ciliary length despite reduced ciliogenesis unexplained\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether and how the immune-regulatory and ciliary-trafficking functions of ARL16 are mechanistically related, and what GEFs/GAPs and direct effectors govern its nucleotide cycle in each context, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of ARL16 in either context\", \"Direct ciliary effectors unidentified\", \"Regulators of ARL16 GTP loading unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [0, 1, 2]}\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\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"DDX58\", \"ELMOD1\", \"ELMOD3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}