{"gene":"PF3D7_1442900","run_date":"2026-09-08T14:19:07","timeline":{"discoveries":[{"year":2001,"finding":"P. falciparum encodes a single Sec7 domain-containing ARF-GEF (PF3D7_1442900). A point mutation converting a conserved methionine to isoleucine in helix H of the Sec7 domain was identified in a brefeldin A-resistant parasite line generated by drug selection, establishing a direct link between this residue and brefeldin A sensitivity.","method":"Drug-selection of resistant parasite line followed by sequencing of the Sec7 domain to identify the causative point mutation","journal":"Molecular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — drug-selection phenotype linked to a specific point mutation by sequencing, single lab, single method; causality inferred by correlation at this stage","pmids":["11555294"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2001,"finding":"The single Sec7 domain of PF3D7_1442900 has an unusual structure: two conserved subdomains essential for protein function are separated by an insertion of 146 amino acids not found in other eukaryotic ARF-GEFs.","method":"Sequence analysis and structural comparison of the plasmodial Sec7 domain relative to other eukaryotic Sec7 domains","journal":"Molecular microbiology","confidence":"Low","confidence_rationale":"Tier 4 / Weak — structural inference based solely on sequence/computational analysis, no biochemical or structural validation reported in the abstract","pmids":["11555294"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2004,"finding":"Targeted double cross-over gene replacement of the endogenous Sec7 domain sequences of PF3D7_1442900 with transgenic sequences carrying the Met-to-Ile point mutation in helix H confirmed that this single point mutation is sufficient to confer brefeldin A resistance in P. falciparum. Constructs lacking the 146 amino acid insertion sequence failed to produce resistant parasites, indicating the insertion is required for functional gene replacement.","method":"Transfection with plasmid constructs followed by double cross-over recombination and drug selection for brefeldin A resistance","journal":"Molecular and biochemical parasitology","confidence":"High","confidence_rationale":"Tier 2 / Strong — targeted allelic replacement with genetic confirmation of double cross-over, causality of specific point mutation established; replicated the initial correlative finding with a direct genetic experiment","pmids":["15500915"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2020,"finding":"The Sec7 domain of PF3D7_1442900 (referred to as a Sec7 domain-containing protein) was not directly tested for GDP/GTP exchange activity on PfArf1 in this study; instead, the human ARNO Sec7 domain was used as a surrogate. The paper established that PfArf1 can be activated by the ARNO Sec7 domain and deactivated by ArfGAP domains in vitro, but ArfGEF-mediated (PF3D7_1442900-mediated) activation of PfArf1 was noted as not yet demonstrated.","method":"In vitro colorimetric microtiter plate-based GTPase assay using truncated PfArf1 and heterologous Sec7/GAP domains","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — in vitro assay established PfArf1 can be activated by a Sec7 domain, but the Sec7 domain used was from human ARNO, not PF3D7_1442900; no direct functional demonstration of PF3D7_1442900 enzymatic activity","pmids":["32144363"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1442900 is the sole ARF-GEF encoded in the P. falciparum genome; its Sec7 domain contains an unusual 146-amino-acid insertion separating two functionally essential subdomains, and a conserved methionine in helix H of the Sec7 domain confers brefeldin A sensitivity, as demonstrated by allelic replacement showing that a Met-to-Ile substitution at this position is sufficient to render parasites resistant to brefeldin A, implicating PF3D7_1442900 as the primary target of brefeldin A in the parasite secretory pathway."},"narrative":{"mechanistic_narrative":"PF3D7_1442900 is the single Sec7 domain-containing ARF-GEF encoded in the P. falciparum genome and functions as the primary target of the secretory-pathway inhibitor brefeldin A in the parasite [PMID:11555294]. A conserved methionine in helix H of its Sec7 domain governs brefeldin A sensitivity: allelic replacement of the endogenous locus with a construct carrying a single Met-to-Ile substitution at this residue is sufficient to render parasites brefeldin A-resistant, establishing PF3D7_1442900 as the drug's molecular target [PMID:11555294, PMID:15500915]. The Sec7 domain is structurally atypical, with two conserved subdomains separated by a 146-amino-acid insertion not found in other eukaryotic ARF-GEFs; gene-replacement constructs lacking this insertion failed to yield viable resistant parasites, indicating the insertion is required for the protein's function [PMID:11555294, PMID:15500915]. Direct GDP/GTP exchange activity of PF3D7_1442900 on its presumptive substrate PfArf1 has not been demonstrated in the available corpus; in vitro activation of PfArf1 has only been shown using a heterologous human ARNO Sec7 domain as a surrogate [PMID:32144363].","teleology":[{"year":2001,"claim":"Establishing whether Plasmodium encodes an ARF-GEF and linking it to drug action, the identification of a single Sec7-domain ARF-GEF and a helix H point mutation in a brefeldin A-resistant line first implicated PF3D7_1442900 as the parasite's brefeldin A target.","evidence":"drug-selection of a brefeldin A-resistant parasite line followed by Sec7-domain sequencing","pmids":["11555294"],"confidence":"Medium","gaps":["Causality inferred by correlation, not yet by genetic replacement","Enzymatic ARF-GEF activity of the protein not tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2001,"claim":"Defining the domain architecture, sequence analysis revealed an unusual 146-amino-acid insertion splitting the two conserved subdomains of the Sec7 domain, distinguishing PF3D7_1442900 from other eukaryotic ARF-GEFs.","evidence":"sequence and structural comparison of the plasmodial Sec7 domain against other eukaryotic Sec7 domains","pmids":["11555294"],"confidence":"Low","gaps":["Structural inference from sequence only, no biochemical or structural validation","Functional role of the insertion untested at this stage"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2004,"claim":"Converting correlation into causation, targeted allelic replacement showed the single Met-to-Ile helix H mutation is sufficient for brefeldin A resistance, and that constructs lacking the 146-aa insertion fail, establishing the insertion as required for function.","evidence":"double cross-over gene replacement of the endogenous Sec7 domain with mutant transgenic sequences followed by brefeldin A selection","pmids":["15500915"],"confidence":"High","gaps":["Does not demonstrate the protein's GDP/GTP exchange activity","Molecular basis of insertion requirement not resolved","Substrate ARF and downstream secretory role not directly assayed"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2020,"claim":"Testing whether the ARF-GEF activates PfArf1, an in vitro study established that PfArf1 can be activated by a Sec7 domain but used the human ARNO domain as a surrogate, leaving PF3D7_1442900's own catalytic activity undemonstrated.","evidence":"in vitro colorimetric GTPase assay with truncated PfArf1 and heterologous Sec7/GAP domains","pmids":["32144363"],"confidence":"Low","gaps":["The Sec7 domain used was heterologous (human ARNO), not PF3D7_1442900","No direct enzymatic demonstration of PF3D7_1442900 activity on PfArf1"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The intrinsic ARF-GEF catalytic activity of PF3D7_1442900, its authentic parasite ARF substrate, its subcellular localization, and the mechanistic function of its 146-amino-acid Sec7 insertion remain undetermined in the available corpus.","evidence":"no direct enzymatic or localization study of PF3D7_1442900 reported","pmids":[],"confidence":"Low","gaps":["No direct measurement of PF3D7_1442900-mediated nucleotide exchange","Localization within the secretory pathway not experimentally established","Function of the 146-aa insertion at the molecular level unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["PFARF1 (PRESUMPTIVE SUBSTRATE; DIRECT ACTIVATION BY PF3D7_1442900 NOT DEMONSTRATED) [#3]"],"other_free_text":["Single Sec7 domain-containing ARF-GEF of P. falciparum [#0]","Primary molecular target of brefeldin A; sensitivity conferred by a conserved methionine in helix H of the Sec7 domain [#0, #2]","Sec7 domain contains an atypical 146-amino-acid insertion separating two conserved subdomains, required for functional gene replacement [#1, #2]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"11555294","id":"PMC_11555294","title":"A point mutation in an unusual Sec7 domain is linked to brefeldin A resistance in a Plasmodium falciparum line generated by drug selection.","date":"2001","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/11555294","citation_count":21,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ARFGEF","Sec7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"15500915","id":"PMC_15500915","title":"Double cross-over gene replacement within the sec 7 domain of a GDP-GTP exchange factor from Plasmodium falciparum allows the generation of a transgenic brefeldin A-resistant parasite line.","date":"2004","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/15500915","citation_count":8,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ARFGEF"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"32144363","id":"PMC_32144363","title":"Detection of the in vitro modulation of Plasmodium falciparum Arf1 by Sec7 and ArfGAP domains using a colorimetric plate-based assay.","date":"2020","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/32144363","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ARFGEF","Sec7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4339,"output_tokens":1294,"usd":0.016213,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6189,"output_tokens":2234,"usd":0.043397,"stage2_stop_reason":"end_turn"},"total_usd":0.05961,"stage1_batch_id":"msgbatch_011BPjN2BL33F8cJXD1r7V7T","stage2_batch_id":"msgbatch_01Qwg6vP7qxkpL6Gsc7tajsb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"P. falciparum encodes a single Sec7 domain-containing ARF-GEF (PF3D7_1442900). A point mutation converting a conserved methionine to isoleucine in helix H of the Sec7 domain was identified in a brefeldin A-resistant parasite line generated by drug selection, establishing a direct link between this residue and brefeldin A sensitivity.\",\n      \"method\": \"Drug-selection of resistant parasite line followed by sequencing of the Sec7 domain to identify the causative point mutation\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — drug-selection phenotype linked to a specific point mutation by sequencing, single lab, single method; causality inferred by correlation at this stage\",\n      \"pmids\": [\"11555294\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"The single Sec7 domain of PF3D7_1442900 has an unusual structure: two conserved subdomains essential for protein function are separated by an insertion of 146 amino acids not found in other eukaryotic ARF-GEFs.\",\n      \"method\": \"Sequence analysis and structural comparison of the plasmodial Sec7 domain relative to other eukaryotic Sec7 domains\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — structural inference based solely on sequence/computational analysis, no biochemical or structural validation reported in the abstract\",\n      \"pmids\": [\"11555294\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Targeted double cross-over gene replacement of the endogenous Sec7 domain sequences of PF3D7_1442900 with transgenic sequences carrying the Met-to-Ile point mutation in helix H confirmed that this single point mutation is sufficient to confer brefeldin A resistance in P. falciparum. Constructs lacking the 146 amino acid insertion sequence failed to produce resistant parasites, indicating the insertion is required for functional gene replacement.\",\n      \"method\": \"Transfection with plasmid constructs followed by double cross-over recombination and drug selection for brefeldin A resistance\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — targeted allelic replacement with genetic confirmation of double cross-over, causality of specific point mutation established; replicated the initial correlative finding with a direct genetic experiment\",\n      \"pmids\": [\"15500915\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The Sec7 domain of PF3D7_1442900 (referred to as a Sec7 domain-containing protein) was not directly tested for GDP/GTP exchange activity on PfArf1 in this study; instead, the human ARNO Sec7 domain was used as a surrogate. The paper established that PfArf1 can be activated by the ARNO Sec7 domain and deactivated by ArfGAP domains in vitro, but ArfGEF-mediated (PF3D7_1442900-mediated) activation of PfArf1 was noted as not yet demonstrated.\",\n      \"method\": \"In vitro colorimetric microtiter plate-based GTPase assay using truncated PfArf1 and heterologous Sec7/GAP domains\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — in vitro assay established PfArf1 can be activated by a Sec7 domain, but the Sec7 domain used was from human ARNO, not PF3D7_1442900; no direct functional demonstration of PF3D7_1442900 enzymatic activity\",\n      \"pmids\": [\"32144363\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1442900 is the sole ARF-GEF encoded in the P. falciparum genome; its Sec7 domain contains an unusual 146-amino-acid insertion separating two functionally essential subdomains, and a conserved methionine in helix H of the Sec7 domain confers brefeldin A sensitivity, as demonstrated by allelic replacement showing that a Met-to-Ile substitution at this position is sufficient to render parasites resistant to brefeldin A, implicating PF3D7_1442900 as the primary target of brefeldin A in the parasite secretory pathway.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1442900 is the single Sec7 domain-containing ARF-GEF encoded in the P. falciparum genome and functions as the primary target of the secretory-pathway inhibitor brefeldin A in the parasite [#0]. A conserved methionine in helix H of its Sec7 domain governs brefeldin A sensitivity: allelic replacement of the endogenous locus with a construct carrying a single Met-to-Ile substitution at this residue is sufficient to render parasites brefeldin A-resistant, establishing PF3D7_1442900 as the drug's molecular target [#0, #2]. The Sec7 domain is structurally atypical, with two conserved subdomains separated by a 146-amino-acid insertion not found in other eukaryotic ARF-GEFs; gene-replacement constructs lacking this insertion failed to yield viable resistant parasites, indicating the insertion is required for the protein's function [#1, #2]. Direct GDP/GTP exchange activity of PF3D7_1442900 on its presumptive substrate PfArf1 has not been demonstrated in the available corpus; in vitro activation of PfArf1 has only been shown using a heterologous human ARNO Sec7 domain as a surrogate [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Establishing whether Plasmodium encodes an ARF-GEF and linking it to drug action, the identification of a single Sec7-domain ARF-GEF and a helix H point mutation in a brefeldin A-resistant line first implicated PF3D7_1442900 as the parasite's brefeldin A target.\",\n      \"evidence\": \"drug-selection of a brefeldin A-resistant parasite line followed by Sec7-domain sequencing\",\n      \"pmids\": [\"11555294\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causality inferred by correlation, not yet by genetic replacement\", \"Enzymatic ARF-GEF activity of the protein not tested\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Defining the domain architecture, sequence analysis revealed an unusual 146-amino-acid insertion splitting the two conserved subdomains of the Sec7 domain, distinguishing PF3D7_1442900 from other eukaryotic ARF-GEFs.\",\n      \"evidence\": \"sequence and structural comparison of the plasmodial Sec7 domain against other eukaryotic Sec7 domains\",\n      \"pmids\": [\"11555294\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Structural inference from sequence only, no biochemical or structural validation\", \"Functional role of the insertion untested at this stage\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Converting correlation into causation, targeted allelic replacement showed the single Met-to-Ile helix H mutation is sufficient for brefeldin A resistance, and that constructs lacking the 146-aa insertion fail, establishing the insertion as required for function.\",\n      \"evidence\": \"double cross-over gene replacement of the endogenous Sec7 domain with mutant transgenic sequences followed by brefeldin A selection\",\n      \"pmids\": [\"15500915\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not demonstrate the protein's GDP/GTP exchange activity\", \"Molecular basis of insertion requirement not resolved\", \"Substrate ARF and downstream secretory role not directly assayed\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Testing whether the ARF-GEF activates PfArf1, an in vitro study established that PfArf1 can be activated by a Sec7 domain but used the human ARNO domain as a surrogate, leaving PF3D7_1442900's own catalytic activity undemonstrated.\",\n      \"evidence\": \"in vitro colorimetric GTPase assay with truncated PfArf1 and heterologous Sec7/GAP domains\",\n      \"pmids\": [\"32144363\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"The Sec7 domain used was heterologous (human ARNO), not PF3D7_1442900\", \"No direct enzymatic demonstration of PF3D7_1442900 activity on PfArf1\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The intrinsic ARF-GEF catalytic activity of PF3D7_1442900, its authentic parasite ARF substrate, its subcellular localization, and the mechanistic function of its 146-amino-acid Sec7 insertion remain undetermined in the available corpus.\",\n      \"evidence\": \"no direct enzymatic or localization study of PF3D7_1442900 reported\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct measurement of PF3D7_1442900-mediated nucleotide exchange\", \"Localization within the secretory pathway not experimentally established\", \"Function of the 146-aa insertion at the molecular level unknown\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005086\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005085\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0046907\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PfArf1 (presumptive substrate; direct activation by PF3D7_1442900 not demonstrated) [#3]\"],\n    \"other_free_text\": [\n      \"Single Sec7 domain-containing ARF-GEF of P. falciparum [#0]\",\n      \"Primary molecular target of brefeldin A; sensitivity conferred by a conserved methionine in helix H of the Sec7 domain [#0, #2]\",\n      \"Sec7 domain contains an atypical 146-amino-acid insertion separating two conserved subdomains, required for functional gene replacement [#1, #2]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1442900","name":null,"product":"Sec7 domain-containing protein ARFGEF, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1306800","name":null,"product":"Sec7 domain-containing protein ARFGEF, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1239400","name":null,"product":"Sec7 domain-containing protein ARFGEF, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"ARFGEF","evaluation":null}