{"gene":"TG_318610","gene_symbol":"AP2IV3","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2017,"finding":"AP2IV-3 functions as a transcriptional activator of bradyzoite development: deletion of AP2IV-3 decreased tissue cyst formation, while conditional overexpression increased it. AP2IV-3 directly regulates the BAG1 promoter (shown by luciferase reporter assay and chromatin immunoprecipitation), and its transcriptional activator function opposes the repressor function of AP2IX-9 on a shared set of bradyzoite target genes.","method":"Gene knockout, conditional overexpression (FKBP/Shield-1 system), BAG1 promoter-luciferase reporter assay, chromatin immunoprecipitation, transcriptome profiling","journal":"mSphere","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (KO, OE, reporter assay, ChIP, transcriptomics) in a single focused study; KO and OE phenotypes are reciprocal and consistent","pmids":["28251183"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"finding":"AP2IV-3 protein expression is induced during alkaline-stress-driven bradyzoite development, peaking after AP2IX-9 expression has begun to decline, placing AP2IV-3 temporally downstream of AP2IX-9 in the transcriptional cascade that controls bradyzoite differentiation.","method":"Immunofluorescence and western blot time-course during alkaline-stress-induced differentiation","journal":"mSphere","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct protein-level time-course data, single lab, corroborated by functional phenotype data in same study","pmids":["28251183"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2010,"finding":"AP2IV-3 mRNA exhibits a cyclical expression profile in dividing tachyzoites, with peak expression occurring during the S/M-subtranscriptome phase of the tachyzoite cell cycle, placing it in a series of ~24 AP2 transcription factors that show successive sharp peaks during the cell cycle.","method":"Genome-wide cell cycle transcriptome profiling (microarray) of synchronized tachyzoites","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — genome-wide transcriptomic approach, replicated across the cell cycle with protein-level confirmation for the AP2 family as a group","pmids":["20865045"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"AP2IV-3 is a nuclear ApiAP2 transcription factor that acts as a transcriptional activator of bradyzoite-specific genes (including BAG1) by directly binding the BAG1 promoter; it is induced during alkaline-stress-driven bradyzoite development and functionally antagonizes the repressor AP2IX-9 to promote tissue cyst formation, while its expression is also cell cycle-regulated in tachyzoites with a peak during S/M phase."},"narrative":{"mechanistic_narrative":"AP2IV-3 is a nuclear ApiAP2 transcription factor in Toxoplasma gondii that acts as a transcriptional activator driving bradyzoite (tissue cyst) development [PMID:28251183]. Deletion of AP2IV-3 reduces tissue cyst formation while conditional overexpression increases it, and the factor directly binds and activates the BAG1 promoter, functionally opposing the repressor AP2IX-9 on a shared set of bradyzoite target genes [PMID:28251183]. AP2IV-3 protein is induced during alkaline-stress-driven differentiation, peaking after AP2IX-9 has begun to decline, placing it temporally downstream in the differentiation cascade [PMID:28251183]. In dividing tachyzoites its mRNA is cell-cycle-regulated, peaking during the S/M phase [PMID:20865045]. Beyond this activator role in bradyzoite gene expression, no additional mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2010,"claim":"Before its function was known, AP2IV-3 was placed within the periodic regulatory program of the tachyzoite cell cycle, establishing it as one of a series of AP2 factors with tightly phased expression.","evidence":"Genome-wide cell cycle transcriptome profiling (microarray) of synchronized tachyzoites","pmids":["20865045"],"confidence":"Medium","gaps":["mRNA periodicity does not establish protein-level dynamics or transcriptional targets","no functional role assigned at this stage","does not connect cell-cycle expression to bradyzoite differentiation"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"claim":"The question of what AP2IV-3 does was answered by showing it is a transcriptional activator of bradyzoite development that directly regulates the BAG1 promoter and antagonizes the repressor AP2IX-9.","evidence":"Gene knockout, conditional overexpression (FKBP/Shield-1), BAG1 promoter-luciferase reporter, chromatin immunoprecipitation, and transcriptome profiling in T. gondii","pmids":["28251183"],"confidence":"High","gaps":["genome-wide direct binding sites beyond BAG1 not mapped","the biochemical basis of antagonism with AP2IX-9 (competition, co-occupancy, or mutual exclusion) not resolved","no structural or DNA-motif characterization of AP2IV-3 binding"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"claim":"The temporal placement of AP2IV-3 in the differentiation cascade was defined by showing its protein induction follows the decline of AP2IX-9 during alkaline stress.","evidence":"Immunofluorescence and western blot time-course during alkaline-stress-induced differentiation","pmids":["28251183"],"confidence":"Medium","gaps":["upstream signals that induce AP2IV-3 expression not identified","temporal ordering shown in a single differentiation model (alkaline stress)"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"How AP2IV-3 cell-cycle-regulated expression in tachyzoites relates mechanistically to its bradyzoite activator function, and its full genome-wide target repertoire, remain open.","evidence":"","pmids":[],"confidence":"Low","gaps":["no genome-wide occupancy map for AP2IV-3","molecular mechanism of AP2IV-3/AP2IX-9 antagonism unresolved","connection between S/M-phase expression and differentiation role unexplained"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["AP2IX-9 (FUNCTIONAL ANTAGONIST ON SHARED BRADYZOITE TARGET GENES)"],"other_free_text":["Directly binds and activates the BAG1 promoter","Expression induced by alkaline stress during bradyzoite differentiation, peaking after AP2IX-9 declines","mRNA cell-cycle-regulated in tachyzoites with an S/M-phase peak"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"20865045","id":"PMC_20865045","title":"Coordinated progression through two subtranscriptomes underlies the tachyzoite cycle of Toxoplasma gondii.","date":"2010","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/20865045","citation_count":234,"is_preprint":false},{"pmid":"28251183","id":"PMC_28251183","title":"Opposing Transcriptional Mechanisms Regulate Toxoplasma Development.","date":"2017","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/28251183","citation_count":68,"is_preprint":false},{"pmid":"29932347","id":"PMC_29932347","title":"The Epigenome, Cell Cycle, and Development in Toxoplasma.","date":"2018","source":"Annual review of microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/29932347","citation_count":51,"is_preprint":false},{"pmid":"20657661","id":"PMC_20657661","title":"The construction and use of log-odds substitution scores for multiple sequence alignment.","date":"2010","source":"PLoS computational biology","url":"https://pubmed.ncbi.nlm.nih.gov/20657661","citation_count":48,"is_preprint":false},{"pmid":"19146987","id":"PMC_19146987","title":"Repeated secondary loss of adaptin complex genes in the Apicomplexa.","date":"2008","source":"Parasitology international","url":"https://pubmed.ncbi.nlm.nih.gov/19146987","citation_count":36,"is_preprint":false},{"pmid":"22486860","id":"PMC_22486860","title":"Cactin is essential for G1 progression in Toxoplasma gondii.","date":"2012","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/22486860","citation_count":23,"is_preprint":false},{"pmid":"25393307","id":"PMC_25393307","title":"Distinct strains of Toxoplasma gondii feature divergent transcriptomes regardless of developmental stage.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/25393307","citation_count":22,"is_preprint":false},{"pmid":"18983845","id":"PMC_18983845","title":"New eukaryotic systematics: a phylogenetic perspective of developmental gene expression in the Apicomplexa.","date":"2008","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/18983845","citation_count":12,"is_preprint":false},{"pmid":"39690155","id":"PMC_39690155","title":"Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/39690155","citation_count":9,"is_preprint":false},{"pmid":"36178892","id":"PMC_36178892","title":"Genomic insights into host and parasite interactions during intracellular infection by Toxoplasma gondii.","date":"2022","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/36178892","citation_count":2,"is_preprint":false},{"pmid":"40934260","id":"PMC_40934260","title":"HIV-1 Tat favors the multiplication of Mycobacterium tuberculosis and Toxoplasma by inhibiting clathrin-mediated endocytosis and autophagy.","date":"2025","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/40934260","citation_count":0,"is_preprint":false},{"pmid":"42087241","id":"PMC_42087241","title":"Host-cell dependent epigenetic profiles associated with survival outcomes in T. gondii infection.","date":"2026","source":"Epigenetics & chromatin","url":"https://pubmed.ncbi.nlm.nih.gov/42087241","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":20110,"output_tokens":912,"usd":0.037005,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5768,"output_tokens":2101,"usd":0.040683,"stage2_stop_reason":"end_turn"},"total_usd":0.077688,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","note":"batch pricing = 50% of standard","corrective_rerun":"2026-09-10 wrong-gene rerun (round-4 rules)","corrective_reason":"paper list: removed papers about other genes"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"AP2IV-3 functions as a transcriptional activator of bradyzoite development: deletion of AP2IV-3 decreased tissue cyst formation, while conditional overexpression increased it. AP2IV-3 directly regulates the BAG1 promoter (shown by luciferase reporter assay and chromatin immunoprecipitation), and its transcriptional activator function opposes the repressor function of AP2IX-9 on a shared set of bradyzoite target genes.\",\n      \"method\": \"Gene knockout, conditional overexpression (FKBP/Shield-1 system), BAG1 promoter-luciferase reporter assay, chromatin immunoprecipitation, transcriptome profiling\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (KO, OE, reporter assay, ChIP, transcriptomics) in a single focused study; KO and OE phenotypes are reciprocal and consistent\",\n      \"pmids\": [\"28251183\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"AP2IV-3 protein expression is induced during alkaline-stress-driven bradyzoite development, peaking after AP2IX-9 expression has begun to decline, placing AP2IV-3 temporally downstream of AP2IX-9 in the transcriptional cascade that controls bradyzoite differentiation.\",\n      \"method\": \"Immunofluorescence and western blot time-course during alkaline-stress-induced differentiation\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct protein-level time-course data, single lab, corroborated by functional phenotype data in same study\",\n      \"pmids\": [\"28251183\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"AP2IV-3 mRNA exhibits a cyclical expression profile in dividing tachyzoites, with peak expression occurring during the S/M-subtranscriptome phase of the tachyzoite cell cycle, placing it in a series of ~24 AP2 transcription factors that show successive sharp peaks during the cell cycle.\",\n      \"method\": \"Genome-wide cell cycle transcriptome profiling (microarray) of synchronized tachyzoites\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — genome-wide transcriptomic approach, replicated across the cell cycle with protein-level confirmation for the AP2 family as a group\",\n      \"pmids\": [\"20865045\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"AP2IV-3 is a nuclear ApiAP2 transcription factor that acts as a transcriptional activator of bradyzoite-specific genes (including BAG1) by directly binding the BAG1 promoter; it is induced during alkaline-stress-driven bradyzoite development and functionally antagonizes the repressor AP2IX-9 to promote tissue cyst formation, while its expression is also cell cycle-regulated in tachyzoites with a peak during S/M phase.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"AP2IV-3 is a nuclear ApiAP2 transcription factor in Toxoplasma gondii that acts as a transcriptional activator driving bradyzoite (tissue cyst) development [#0]. Deletion of AP2IV-3 reduces tissue cyst formation while conditional overexpression increases it, and the factor directly binds and activates the BAG1 promoter, functionally opposing the repressor AP2IX-9 on a shared set of bradyzoite target genes [#0]. AP2IV-3 protein is induced during alkaline-stress-driven differentiation, peaking after AP2IX-9 has begun to decline, placing it temporally downstream in the differentiation cascade [#1]. In dividing tachyzoites its mRNA is cell-cycle-regulated, peaking during the S/M phase [#2]. Beyond this activator role in bradyzoite gene expression, no additional mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Before its function was known, AP2IV-3 was placed within the periodic regulatory program of the tachyzoite cell cycle, establishing it as one of a series of AP2 factors with tightly phased expression.\",\n      \"evidence\": \"Genome-wide cell cycle transcriptome profiling (microarray) of synchronized tachyzoites\",\n      \"pmids\": [\n        \"20865045\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"mRNA periodicity does not establish protein-level dynamics or transcriptional targets\",\n        \"no functional role assigned at this stage\",\n        \"does not connect cell-cycle expression to bradyzoite differentiation\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"The question of what AP2IV-3 does was answered by showing it is a transcriptional activator of bradyzoite development that directly regulates the BAG1 promoter and antagonizes the repressor AP2IX-9.\",\n      \"evidence\": \"Gene knockout, conditional overexpression (FKBP/Shield-1), BAG1 promoter-luciferase reporter, chromatin immunoprecipitation, and transcriptome profiling in T. gondii\",\n      \"pmids\": [\n        \"28251183\"\n      ],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"genome-wide direct binding sites beyond BAG1 not mapped\",\n        \"the biochemical basis of antagonism with AP2IX-9 (competition, co-occupancy, or mutual exclusion) not resolved\",\n        \"no structural or DNA-motif characterization of AP2IV-3 binding\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"The temporal placement of AP2IV-3 in the differentiation cascade was defined by showing its protein induction follows the decline of AP2IX-9 during alkaline stress.\",\n      \"evidence\": \"Immunofluorescence and western blot time-course during alkaline-stress-induced differentiation\",\n      \"pmids\": [\n        \"28251183\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"upstream signals that induce AP2IV-3 expression not identified\",\n        \"temporal ordering shown in a single differentiation model (alkaline stress)\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How AP2IV-3 cell-cycle-regulated expression in tachyzoites relates mechanistically to its bradyzoite activator function, and its full genome-wide target repertoire, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"no genome-wide occupancy map for AP2IV-3\",\n        \"molecular mechanism of AP2IV-3/AP2IX-9 antagonism unresolved\",\n        \"connection between S/M-phase expression and differentiation role unexplained\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0001228\",\n        \"supporting_discovery_ids\": [\n          0\n        ],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      },\n      {\n        \"term_id\": \"GO:0000976\",\n        \"supporting_discovery_ids\": [\n          0\n        ],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0005634\",\n        \"supporting_discovery_ids\": [\n          0,\n          1\n        ],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0030154\",\n        \"supporting_discovery_ids\": [\n          0,\n          1\n        ],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"AP2IX-9 (functional antagonist on shared bradyzoite target genes)\"\n    ],\n    \"other_free_text\": [\n      \"Directly binds and activates the BAG1 promoter\",\n      \"Expression induced by alkaline stress during bradyzoite differentiation, peaking after AP2IX-9 declines\",\n      \"mRNA cell-cycle-regulated in tachyzoites with an S/M-phase peak\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_318610","name":"AP2IV3","product":"AP2 domain transcription factor AP2IV-3","uniprot_acc":"A0A125YJZ2","chromosome":"TGME49_chrIV","start_pos":1191647},{"strain":"GT1","gene_id":"TGGT1_318610","name":null,"product":"AP2 domain transcription factor AP2IV-3","uniprot_acc":null,"chromosome":"TGGT1_chrIV","start_pos":1134392},{"strain":"RH88","gene_id":"TGRH88_007930","name":null,"product":"AP2 domain transcription factor AP2IV-3","uniprot_acc":null,"chromosome":"CM023085","start_pos":1214726},{"strain":"VEG","gene_id":"TGVEG_318610","name":null,"product":"AP2 domain transcription factor AP2IV-3","uniprot_acc":"B9QI50","chromosome":"TGVEG_chrIV","start_pos":1202291}]}