Affinage

ARF3

ADP-ribosylation factor 3 · UniProt P61204

Length
181 aa
Mass
20.6 kDa
Annotated
2026-06-09
30 papers in source corpus 10 papers cited in narrative 10 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ARF3 is a small GTPase that cycles between inactive GDP-bound and active GTP-bound states to govern membrane trafficking at the trans-Golgi network and recycling endosomes (PMID:8917509, PMID:20357002, PMID:22971977). Its activation is catalyzed by Sec7-domain, brefeldin A-inhibited guanine nucleotide exchange factors of the BIG family purified from brain cytosol, and ARF3 depends uniquely on BIG GEFs for its temperature-sensitive recruitment to TGN membranes, distinguishing it from the closely related ARF1 (PMID:8917509, PMID:20357002). A hydrophobic pocket formed by F51, W66, and Y81 in the GDP-bound state, together with residues at opposite ends of the protein, tunes nucleotide exchange kinetics, membrane recruitment, and effector selection (PMID:11150519, PMID:20357002). Functionally, ARF3 acts redundantly with ARF1 to maintain recycling endosome integrity and transferrin recycling to the plasma membrane, and both class I ARFs localize to the Flemming body where they are required for completion of cytokinesis (PMID:22971977, PMID:26330566). ARF3 also controls collective cancer cell invasion modality and metastatic behavior by associating with and regulating turnover of N-cadherin (PMID:36880595), and acts downstream of BIG1 in macrophages to drive PI(4,5)P2 synthesis and TIRAP recruitment that support TLR4-MyD88 inflammatory signaling (PMID:32415087). De novo missense variants in ARF3 that perturb GTP/GDP binding, GGA1 effector binding, and Golgi morphology cause a neurodevelopmental disorder, with both loss-of-function and gain-of-function alleles disrupting brain development in zebrafish and Drosophila models (PMID:34346499, PMID:36369169).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 1996 High

    Established that ARF3 nucleotide exchange is not spontaneous but catalyzed by a defined enzyme class, identifying a Sec7-domain GEP as the activator and explaining the brefeldin A sensitivity of ARF3-dependent trafficking.

    Evidence Protein purification of a ~200 kDa GEP from bovine brain cytosol with in vitro nucleotide exchange assays and tryptic peptide sequencing showing 47% identity to yeast Sec7

    PMID:8917509

    Open questions at the time
    • Did not resolve which specific BIG-family GEF acts on ARF3 in cells
    • Substrate specificity between ARF1 and ARF3 not distinguished
  2. 2000 High

    Defined the structural determinants within ARF3 that control nucleotide exchange kinetics and effector binding, linking specific GDP-pocket residues to functional output.

    Evidence Site-directed mutagenesis of F51/W66/Y81 with in vitro nucleotide dissociation/association assays and yeast two-hybrid effector binding

    PMID:11150519

    Open questions at the time
    • Effector identities defined only by two-hybrid, not in cells
    • No structural model of the GDP-bound pocket provided
  3. 2010 High

    Resolved how ARF3 is targeted to a specific membrane compartment, showing its TGN localization uniquely requires BIG GEFs and is governed by distinct residues controlling recruitment versus temperature-dependent release.

    Evidence siRNA knockdown of BIG GEFs with fluorescence microscopy, temperature-shift block, and ARF3 mutagenesis

    PMID:20357002

    Open questions at the time
    • Mechanism of temperature-dependent release not molecularly defined
    • Functional consequence of ARF3-specific TGN targeting not addressed here
  4. 2012 High

    Assigned ARF3 a functional role in endosomal recycling, showing it acts redundantly with ARF1 to maintain recycling endosome morphology and transferrin return to the plasma membrane.

    Evidence siRNA double knockdown of ARF1 and ARF3 with transferrin recycling, endocytosis, and retrograde transport assays plus compartment markers

    PMID:22971977

    Open questions at the time
    • Redundancy prevents isolation of the ARF3-specific contribution
    • Effectors mediating recycling endosome integrity not identified
  5. 2015 Medium

    Extended ARF3 function to cell division, demonstrating class I ARFs localize to the Flemming body and are required for cytokinesis completion.

    Evidence Double and triple siRNA knockdown with Flemming body localization and multinucleate cell quantification

    PMID:26330566

    Open questions at the time
    • ARF3-specific contribution confounded by combined knockdowns
    • Molecular partners at the Flemming body not identified
  6. 2020 Medium

    Placed ARF3 in an inflammatory signaling axis, showing BIG1-driven ARF3 activation promotes PI(4,5)P2 synthesis and TIRAP recruitment supporting TLR4-MyD88 signaling.

    Evidence Myeloid-specific BIG1 knockout mouse and macrophage knockdowns with ARF3 activation, PI(4,5)P2, TIRAP recruitment, and cytokine assays

    PMID:32415087

    Open questions at the time
    • Direct ARF3 KO epistasis not shown
    • Mechanism linking ARF3 to PIP5K activation not biochemically resolved
  7. 2022 High

    Connected ARF3 dysfunction to human disease, showing de novo variants perturbing the nucleotide-binding pocket and effector binding cause a neurodevelopmental disorder via both loss- and gain-of-function mechanisms.

    Evidence Cell-based Golgi/vesicle and nucleotide binding assays, GGA1 pull-downs, and Drosophila and zebrafish disease modeling across multiple variants

    PMID:34346499 PMID:36369169

    Open questions at the time
    • How distinct alleles produce convergent neurodevelopmental phenotypes unresolved
    • Cell-type-specific requirements in human brain not defined
  8. 2023 Medium

    Revealed a role for ARF3 in cancer cell behavior, identifying N-cadherin turnover as the mechanism by which ARF3 levels set collective invasion modality and metastatic potential.

    Evidence 3D functional genomic screen with siRNA/overexpression, N-cadherin co-association and turnover assays, and intraprostatic in vivo tumor transplants

    PMID:36880595

    Open questions at the time
    • Direct physical mode of ARF3-N-cadherin association not structurally defined
    • Single-lab study not independently replicated
  9. 2025 Low

    Implicated ARF3 in viral pathogenesis, showing its knockdown suppresses influenza A replication and dampens inflammasome-driven lung injury.

    Evidence siRNA knockdown in vitro and mouse IAV pneumonia model with cytokine and NLRP3 inflammasome readouts

    PMID:40608252

    Open questions at the time
    • No direct biochemical mechanism linking ARF3 to NLRP3 inflammasome
    • Single-lab phenotypic study with limited pathway resolution

Open questions

Synthesis pass · forward-looking unresolved questions
  • How ARF3's distinct membrane localization and effector selectivity translate into its non-redundant roles in neurodevelopment, cancer invasion, and inflammation remains unresolved.
  • No structure of ARF3 with its GEFs or effectors in the timeline
  • ARF3-specific (vs ARF1) effector repertoire not comprehensively mapped
  • Causal chain from GTPase cycle to PI(4,5)P2 synthesis and N-cadherin turnover not biochemically reconstituted

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003924 GTPase activity 3
Localization
GO:0005794 Golgi apparatus 3 GO:0005768 endosome 1 GO:0005829 cytosol 1
Pathway
R-HSA-1266738 Developmental Biology 2 R-HSA-5653656 Vesicle-mediated transport 2 R-HSA-1640170 Cell Cycle 1 R-HSA-168256 Immune System 1

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1996 A BFA-inhibited guanine nucleotide exchange protein (GEP) for ARF1 and ARF3 was purified from bovine brain cytosol as a ~200 kDa protein containing tryptic peptides 47% identical to yeast Sec7, establishing that ARF3 GDP-to-GTP exchange is catalyzed by a Sec7-domain-containing GEP and is sensitive to brefeldin A. Protein purification from bovine brain cytosol (DEAE-Sephacel, hydroxylapatite, Mono Q, Superose 6), SDS/PAGE, silver staining, electroelution/renaturation, in vitro nucleotide exchange activity assay, tryptic peptide sequencing Proceedings of the National Academy of Sciences of the United States of America High 8917509
2000 Three residues of human ARF3 (F51, W66, Y81) form a hydrophobic pocket in the GDP-bound state; mutations at these residues increased the rate of GDP dissociation and association but not GTPγS binding, and selectively impaired binding to different ARF effectors in two-hybrid assays, indicating these residues regulate nucleotide exchange kinetics and effector interactions. Site-directed mutagenesis of ARF3, in vitro nucleotide dissociation/association assays, yeast two-hybrid effector binding assays FEBS letters High 11150519
2010 ARF3 localizes selectively to the trans-Golgi network (TGN) in a manner uniquely dependent on BIG family guanine nucleotide exchange factors; BIGs knockdown redistributes ARF3 but not ARF1 from Golgi membranes, and this TGN association is temperature-sensitive. Mutational analysis identified pairs of residues at opposite ends of ARF3 that separately control membrane recruitment and temperature-dependent release. siRNA knockdown of BIG GEFs, fluorescence microscopy, temperature-shift experiments (20°C block), site-directed mutagenesis of ARF3, phylogenetic analysis Molecular biology of the cell High 20357002
2012 ARF1 and ARF3 localize to endosomal compartments containing endocytosed transferrin, and simultaneous siRNA depletion of both ARF1 and ARF3 induces tubulation of recycling endosomes (Rab4+, Rab11+, TfR+) and suppresses transferrin recycling to the plasma membrane, without affecting Golgi integrity, early/late endosomes, or retrograde TGN transport. siRNA double knockdown of ARF1 and ARF3, EGFP-tagging and fluorescence microscopy, transferrin recycling assay, endocytosis assay, retrograde transport assays (TGN38, CD4-furin, EGF) Cell structure and function High 22971977
2015 Class I ARFs (ARF1 and ARF3) localize to the Flemming body during late cytokinesis; double knockdown of ARF1 and ARF3 increases multinucleate cells, and simultaneous triple knockdown of ARF1, ARF3, and ARF6 causes severe cytokinesis defects. EFA6 exchange factor activates both ARF6 and ARF1 in cells. siRNA knockdown (double and triple), fluorescence microscopy of Flemming body localization, multinucleate cell quantification, cytokinesis assays Journal of biochemistry Medium 26330566
2020 BIG1 (a BFA-inhibited GEF) activates ARF3 in macrophages; BIG1 deficiency inhibits ARF3 activation, reduces PI(4,5)P2 synthesis by impairing PIP5K activation, and prevents TIRAP recruitment to the plasma membrane, thereby suppressing TLR4-MyD88 signaling during LPS stimulation. Myeloid-specific BIG1 knockout mouse, siRNA knockdown in bone marrow-derived macrophages and THP-1 cells, ARF3 activation assay, PI(4,5)P2 measurement, TIRAP recruitment assay, cytokine measurement Cell death & disease Medium 32415087
2021 De novo missense variants in ARF3 (p.Asp67Val and p.Arg99Leu) cause neurodevelopmental disorder. In vitro assays showed p.Asp67Val causes cytosolic dispersal of ARF3 and dispersed Golgi (loss-of-function), while p.Arg99Leu localizes normally to Golgi but shows increased binding to GGA1 (gain-of-function). In vivo, p.Asp67Val expression was lethal in Drosophila, and p.Arg99Leu caused rough eye phenotype similar to known gain-of-function variant p.Gln71Leu. In vitro subcellular localization assays, pull-down assays for GGA1 binding, Drosophila in vivo expression experiments Human molecular genetics High 34346499
2022 De novo missense variants in ARF3 affecting the guanine nucleotide binding pocket variably perturb protein stability and GTP/GDP binding, disrupt Golgi morphology and vesicle assembly/trafficking in cell-based assays, and in zebrafish models cause dominant effects on brain size (microcephaly) and body plan formation, impairing neural precursor proliferation and planar cell polarity-dependent cell movements. Cell-based assays (Golgi morphology, vesicle trafficking), nucleotide binding assays, zebrafish disease modeling, in vivo analysis of neural precursor proliferation and cell polarity Nature communications High 36369169
2023 ARF3 controls the modality of collective cancer cell invasion by associating with and regulating the turnover of N-cadherin; ARF3 loss or gain switches between leader-cell-led chain invasion and collective sheet movement. In vivo, ARF3 levels act as a rheostat for metastasis from intraprostatic tumor transplants. Functional genomic screen of 3D prostate cancer cell behavior, siRNA/overexpression, N-cadherin co-association and turnover assays, intraprostatic in vivo tumor transplant model The Journal of cell biology Medium 36880595
2025 ARF3 knockdown in mice and cells suppressed influenza A virus (H3N2) replication in vitro and mitigated IAV-induced lung injury in vivo, reducing pro-inflammatory cytokines and attenuating NLRP3 inflammasome activation. siRNA knockdown in vitro, mouse IAV pneumonia model, cytokine measurement, NLRP3 inflammasome activation assay Virus genes Low 40608252

Source papers

Stage 0 corpus · 30 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1996 Isolation of a brefeldin A-inhibited guanine nucleotide-exchange protein for ADP ribosylation factor (ARF) 1 and ARF3 that contains a Sec7-like domain. Proceedings of the National Academy of Sciences of the United States of America 131 8917509
2017 The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module. Current biology : CB 76 28552357
2012 ARF1 and ARF3 are required for the integrity of recycling endosomes and the recycling pathway. Cell structure and function 56 22971977
1994 Characterization of a glucose-repressible ADP-ribosylation factor 3 (ARF3) from Saccharomyces cerevisiae. The Journal of biological chemistry 50 8063710
2010 Arf3 is activated uniquely at the trans-Golgi network by brefeldin A-inhibited guanine nucleotide exchange factors. Molecular biology of the cell 48 20357002
2021 Auxin Response Factor 2 (ARF2), ARF3, and ARF4 Mediate Both Lateral Root and Nitrogen Fixing Nodule Development in Medicago truncatula. Frontiers in plant science 32 33897748
2022 Maize miR167-ARF3/30-polyamine oxidase 1 module-regulated H2O2 production confers resistance to maize chlorotic mottle virus. Plant physiology 31 35298645
2012 Non-cell-autonomous regulation of crucifer self-incompatibility by Auxin Response Factor ARF3. Proceedings of the National Academy of Sciences of the United States of America 30 23129621
2015 MicroRNA390-Directed TAS3 Cleavage Leads to the Production of tasiRNA-ARF3/4 During Somatic Embryogenesis in Dimocarpus longan Lour. Frontiers in plant science 28 26734029
2021 De novo ARF3 variants cause neurodevelopmental disorder with brain abnormality. Human molecular genetics 22 34346499
2024 The long noncoding RNA ALEX1 confers a functional phase state of ARF3 to enhance rice resistance to bacterial pathogens. Molecular plant 21 39659014
2007 The Saccharomyces cerevisiae Arf3 protein is involved in actin cable and cortical patch formation. FEMS yeast research 21 17425670
2020 BIG1 controls macrophage pro-inflammatory responses through ARF3-mediated PI(4,5)P2 synthesis. Cell death & disease 20 32415087
2015 Class I Arfs (Arf1 and Arf3) and Arf6 are localized to the Flemming body and play important roles in cytokinesis. Journal of biochemistry 20 26330566
2022 Dominant ARF3 variants disrupt Golgi integrity and cause a neurodevelopmental disorder recapitulated in zebrafish. Nature communications 19 36369169
2007 Identification of a guanine nucleotide exchange factor for Arf3, the yeast orthologue of mammalian Arf6. PloS one 17 17786213
2023 The small GTPase ARF3 controls invasion modality and metastasis by regulating N-cadherin levels. The Journal of cell biology 12 36880595
2020 circ_ARF3 regulates the pathogenesis of osteosarcoma by sponging miR-1299 to maintain CDK6 expression. Cellular signalling 12 32240746
2000 Residues forming a hydrophobic pocket in ARF3 are determinants of GDP dissociation and effector interactions. FEBS letters 10 11150519
2021 ARF3 inhibits proliferation and promotes apoptosis in gastric cancer by regulating AKT and ERK pathway. Acta biochimica Polonica 9 33847108
2021 Genome-Wide Identification of the ARF Gene Family and ARF3 Target Genes Regulating Ovary Initiation in Hazel via ChIP Sequencing. Frontiers in plant science 9 34447403
2024 CircRNA Arf3 suppresses glomerular mesangial cell proliferation and fibrosis in diabetic nephropathy via miR-107-3p/Tmbim6 axis. Journal of bioenergetics and biomembranes 5 39120858
2025 ARF3-mediated auxin signaling is essential for sex determination in cucumber. Science (New York, N.Y.) 4 41379936
2026 Newly identified ARF3 variants strengthen the causal link between Golgi fragmentation and brain malformations. European journal of human genetics : EJHG 1 41507605
2024 Neurodevelopmental disorder associated with gene ARF3: A case report. American journal of medical genetics. Part A 1 38712921
2023 ARF3 weights the balance for prostate cancer metastasis. The Journal of cell biology 1 36920439
2023 A Novel Circ_Arf3/miR-452-5p/Mbnl1 Axis Regulates Proliferation and Expression of Fibrosis-Related Proteins of Mouse Mesangial Cells Under High Glucose. Diabetes, metabolic syndrome and obesity : targets and therapy 1 37457110
2025 ARF3 as a novel biomarker and target in acute myeloid leukemia: Insights from pan-cancer analysis. Genomics 0 39756487
2025 ARF3 knockdown inhibits influenza a virus and virus-induced pneumonia. Virus genes 0 40608252
2025 The tasiR-ARF pathway in plants: origin, functions, and interplay of miR-390, tasiRNAs and ARF3. Plant biology (Stuttgart, Germany) 0 41386637

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