{"gene":"TG_230340","gene_symbol":"AAP4","run_date":"2026-09-08T11:06:50","timeline":{"discoveries":[{"year":2019,"finding":"AAP4 (Apical Annuli Protein 4) is a component of the apical annuli of Toxoplasma gondii, localizing to the largest ring-like structure (~400 nm diameter) within the annuli, which are embedded in the inner membrane complex (IMC) sutures at the apical end of the parasite.","method":"Reciprocal proximity biotinylation (BioID) proteomics and super-resolution microscopy","journal":"Cellular microbiology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal BioID with orthogonal super-resolution microscopy validation, multiple AAPs confirmed in a single rigorous study","pmids":["31470470"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"Knockout of AAP4 modestly decreased parasite fitness in vitro but had no significant impact on acute virulence in vivo, indicating AAP4 is not essential for acute infection.","method":"Genetic knockout with in vitro fitness assay and in vivo mouse virulence assay","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with two distinct readouts (in vitro fitness, in vivo virulence), single lab","pmids":["31470470"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"AAP4 is the most conserved component of the apical annuli and is restricted phylogenetically to coccidian apicomplexans that replicate by internal budding, suggesting a functional link to internal budding replication.","method":"Phylogenetic analysis combined with BioID localization data","journal":"Cellular microbiology","confidence":"Low","confidence_rationale":"Tier 4 / Weak — phylogenetic/computational inference with no direct functional experiment confirming the replication role","pmids":["31470470"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"AAP4 is a coiled-coil protein that constitutes the largest (~400 nm) ring-like structure of the apical annuli, a pore-like complex embedded in the IMC sutures of Toxoplasma gondii; it is conserved among coccidian apicomplexans that use internal budding, contributes modestly to in vitro fitness when knocked out, and is dispensable for acute in vivo virulence."},"narrative":{"mechanistic_narrative":"AAP4 (Apical Annuli Protein 4) is a structural component of the apical annuli of Toxoplasma gondii, pore-like complexes embedded in the inner membrane complex (IMC) sutures at the apical end of the parasite [PMID:31470470]. Within the annuli, AAP4 localizes to the largest (~400 nm diameter) ring-like structure, defining its position as a peripheral scaffolding element of this complex [PMID:31470470]. Genetic knockout produces only a modest reduction of in vitro fitness and does not impair acute virulence in mice, indicating AAP4 is dispensable for acute infection [PMID:31470470]. Beyond its structural assignment within the apical annuli, no biochemical activity or molecular partners for AAP4 have been characterized in the available corpus.","teleology":[{"year":2019,"claim":"Before this work the molecular composition of the apical annuli was undefined; identifying AAP4 as a component localizing to the largest ring established it as a defined structural constituent of this IMC-embedded complex.","evidence":"Reciprocal proximity biotinylation (BioID) proteomics with orthogonal super-resolution microscopy in Toxoplasma gondii","pmids":["31470470"],"confidence":"High","gaps":["No biochemical activity or direct binding partners assigned to AAP4","The function of the apical annuli themselves not resolved","Mechanism by which AAP4 is recruited to the IMC sutures unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"To test whether AAP4 is required for the parasite, knockout was assessed and showed only a modest in vitro fitness cost with no loss of acute virulence, establishing AAP4 as non-essential for acute infection.","evidence":"Genetic knockout with in vitro fitness assay and in vivo mouse virulence assay in Toxoplasma gondii","pmids":["31470470"],"confidence":"Medium","gaps":["Whether AAP4 contributes to chronic infection or other life-cycle stages not tested","Whether other apical annuli proteins functionally compensate not addressed","The cellular process disrupted by loss of AAP4 not identified"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"To place AAP4 in an evolutionary context, phylogenetic analysis found it restricted to coccidian apicomplexans that replicate by internal budding, raising a possible functional link to that replication mode.","evidence":"Phylogenetic analysis combined with BioID localization data","pmids":["31470470"],"confidence":"Low","gaps":["Inference is computational with no direct functional experiment linking AAP4 to internal budding","No mechanistic role in budding demonstrated"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"The biochemical function of AAP4, its direct interaction partners within the apical annuli, and the physiological role of the annuli themselves remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No molecular activity assigned to AAP4","Function of the apical annuli complex not established","Contribution to internal budding untested experimentally"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Apical annuli ring-like structure (~400 nm largest ring)"],"partners":[],"other_free_text":["Phylogenetically restricted to coccidian apicomplexans that replicate by internal budding [#2]","Knockout causes modest in vitro fitness reduction but no loss of acute in vivo virulence [#1]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"31470470","id":"PMC_31470470","title":"The apical annuli of Toxoplasma gondii are composed of coiled-coil and signalling proteins embedded in the inner membrane complex sutures.","date":"2019","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/31470470","citation_count":38,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2950,"output_tokens":758,"usd":0.01011,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5529,"output_tokens":1634,"usd":0.034248,"stage2_stop_reason":"end_turn"},"total_usd":0.044358,"stage1_batch_id":"msgbatch_01WokvBYTB6JLnYrpD4rXnyV","stage2_batch_id":"msgbatch_01M7hsQDvz6AqVC9DLVjQzzc","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"AAP4 (Apical Annuli Protein 4) is a component of the apical annuli of Toxoplasma gondii, localizing to the largest ring-like structure (~400 nm diameter) within the annuli, which are embedded in the inner membrane complex (IMC) sutures at the apical end of the parasite.\",\n      \"method\": \"Reciprocal proximity biotinylation (BioID) proteomics and super-resolution microscopy\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal BioID with orthogonal super-resolution microscopy validation, multiple AAPs confirmed in a single rigorous study\",\n      \"pmids\": [\"31470470\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Knockout of AAP4 modestly decreased parasite fitness in vitro but had no significant impact on acute virulence in vivo, indicating AAP4 is not essential for acute infection.\",\n      \"method\": \"Genetic knockout with in vitro fitness assay and in vivo mouse virulence assay\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with two distinct readouts (in vitro fitness, in vivo virulence), single lab\",\n      \"pmids\": [\"31470470\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"AAP4 is the most conserved component of the apical annuli and is restricted phylogenetically to coccidian apicomplexans that replicate by internal budding, suggesting a functional link to internal budding replication.\",\n      \"method\": \"Phylogenetic analysis combined with BioID localization data\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — phylogenetic/computational inference with no direct functional experiment confirming the replication role\",\n      \"pmids\": [\"31470470\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"AAP4 is a coiled-coil protein that constitutes the largest (~400 nm) ring-like structure of the apical annuli, a pore-like complex embedded in the IMC sutures of Toxoplasma gondii; it is conserved among coccidian apicomplexans that use internal budding, contributes modestly to in vitro fitness when knocked out, and is dispensable for acute in vivo virulence.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"AAP4 (Apical Annuli Protein 4) is a structural component of the apical annuli of Toxoplasma gondii, pore-like complexes embedded in the inner membrane complex (IMC) sutures at the apical end of the parasite [#0]. Within the annuli, AAP4 localizes to the largest (~400 nm diameter) ring-like structure, defining its position as a peripheral scaffolding element of this complex [#0]. Genetic knockout produces only a modest reduction of in vitro fitness and does not impair acute virulence in mice, indicating AAP4 is dispensable for acute infection [#1]. Beyond its structural assignment within the apical annuli, no biochemical activity or molecular partners for AAP4 have been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Before this work the molecular composition of the apical annuli was undefined; identifying AAP4 as a component localizing to the largest ring established it as a defined structural constituent of this IMC-embedded complex.\",\n      \"evidence\": \"Reciprocal proximity biotinylation (BioID) proteomics with orthogonal super-resolution microscopy in Toxoplasma gondii\",\n      \"pmids\": [\"31470470\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No biochemical activity or direct binding partners assigned to AAP4\",\n        \"The function of the apical annuli themselves not resolved\",\n        \"Mechanism by which AAP4 is recruited to the IMC sutures unknown\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"To test whether AAP4 is required for the parasite, knockout was assessed and showed only a modest in vitro fitness cost with no loss of acute virulence, establishing AAP4 as non-essential for acute infection.\",\n      \"evidence\": \"Genetic knockout with in vitro fitness assay and in vivo mouse virulence assay in Toxoplasma gondii\",\n      \"pmids\": [\"31470470\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether AAP4 contributes to chronic infection or other life-cycle stages not tested\",\n        \"Whether other apical annuli proteins functionally compensate not addressed\",\n        \"The cellular process disrupted by loss of AAP4 not identified\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"To place AAP4 in an evolutionary context, phylogenetic analysis found it restricted to coccidian apicomplexans that replicate by internal budding, raising a possible functional link to that replication mode.\",\n      \"evidence\": \"Phylogenetic analysis combined with BioID localization data\",\n      \"pmids\": [\"31470470\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Inference is computational with no direct functional experiment linking AAP4 to internal budding\",\n        \"No mechanistic role in budding demonstrated\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The biochemical function of AAP4, its direct interaction partners within the apical annuli, and the physiological role of the annuli themselves remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No molecular activity assigned to AAP4\",\n        \"Function of the apical annuli complex not established\",\n        \"Contribution to internal budding untested experimentally\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"apical annuli\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"inner membrane complex sutures\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [\"Apical annuli ring-like structure (~400 nm largest ring)\"],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Phylogenetically restricted to coccidian apicomplexans that replicate by internal budding [#2]\",\n      \"Knockout causes modest in vitro fitness reduction but no loss of acute in vivo virulence [#1]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_230340","name":"AAP4","product":"apical annuli protein AAP4","uniprot_acc":"S8GB40","chromosome":"TGME49_chrVIII","start_pos":713792},{"strain":"GT1","gene_id":"TGGT1_230340","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrVIII","start_pos":711206},{"strain":"RH88","gene_id":"TGRH88_074740","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023089","start_pos":5822656},{"strain":"VEG","gene_id":"TGVEG_230340","name":null,"product":"putative high molecular mass nuclear antigen","uniprot_acc":"B9Q5E6","chromosome":"TGVEG_chrVIII","start_pos":720621}]}