{"gene":"TG_261220","gene_symbol":"SPT4","run_date":"2026-09-08T12:58:25","timeline":{"discoveries":[{"year":2019,"finding":"TgSpt4 (a small zinc finger protein) functions in conjunction with TgSpt5 as part of the transcription elongation complex in T. gondii, and together TgSpt4 and TgSpt5 can complement loss-of-function mutations in their yeast counterparts, establishing functional conservation of the Spt4-Spt5 partnership.","method":"Co-immunoprecipitation (TgSpt5–TgSpt4 interaction), yeast complementation assay","journal":"Biochimica et biophysica acta. Gene regulatory mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal interaction demonstrated and orthogonal yeast complementation assay validates function, single lab","pmids":["30707945"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"TgSpt4, as part of the TgSpt4-TgSpt5 complex, is required for transcription elongation; the complex associates with actively transcribed genes and its enrichment toward the 3' end of genes coincides with the P-Ser2 form of RNAPII, a marker of active elongation.","method":"Chromatin immunoprecipitation (ChIP) of TgSpt5; co-localization with P-Ser2 RNAPII","journal":"Biochimica et biophysica acta. Gene regulatory mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and co-localization data from single lab; TgSpt4 role inferred from its interaction partner TgSpt5's direct ChIP evidence","pmids":["30707945"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"TgSpt4 is a small zinc finger protein that partners with TgSpt5 to form a transcription elongation factor complex in Toxoplasma gondii; this complex interacts with the largest subunit of RNA Pol II (TgRpb1), associates with actively transcribed genes enriched at their 3' ends, and is functionally conserved as demonstrated by complementation of yeast spt4/spt5 loss-of-function mutants."},"narrative":{"mechanistic_narrative":"TgSpt4 is a small zinc finger protein that acts as a transcription elongation factor in Toxoplasma gondii by partnering with TgSpt5 to form a heterodimeric complex analogous to the conserved Spt4-Spt5 elongation factor [PMID:30707945]. The functional conservation of this partnership is established by the ability of TgSpt4 and TgSpt5 to complement loss-of-function mutations in their yeast counterparts [PMID:30707945]. As part of this complex, TgSpt4 supports transcription elongation: the complex associates with actively transcribed genes, and its enrichment toward the 3' ends of genes coincides with the P-Ser2 elongating form of RNA polymerase II [PMID:30707945]. Beyond this elongation-factor role defined in the single available study, no further mechanistic detail for TgSpt4 has been characterized in the available corpus.","teleology":[{"year":2019,"claim":"Establishing whether T. gondii possesses a conserved Spt4-Spt5 elongation factor was needed to understand transcription regulation in this parasite; demonstrating physical partnership and cross-species functional rescue answered this.","evidence":"Co-immunoprecipitation showing TgSpt5-TgSpt4 interaction and yeast complementation of spt4/spt5 loss-of-function mutants","pmids":["30707945"],"confidence":"Medium","gaps":["Reciprocal interaction shown but the structural basis of the TgSpt4-TgSpt5 interface is undefined","Direct enzymatic or biochemical activity of TgSpt4 itself not assayed","Single lab, no independent replication"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"Whether the TgSpt4-TgSpt5 complex acts on active transcription was unresolved; genome-wide localization coinciding with elongating polymerase established its role in transcription elongation.","evidence":"ChIP of TgSpt5 showing association with actively transcribed genes and 3'-end enrichment coinciding with P-Ser2 RNAPII","pmids":["30707945"],"confidence":"Medium","gaps":["TgSpt4's specific contribution inferred from its partner TgSpt5's direct ChIP evidence rather than measured directly","Mechanism by which the complex is recruited to elongating polymerase not defined","Loss-of-function phenotype for TgSpt4 in the parasite not established"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"How TgSpt4 loss affects parasite viability, gene-specific transcription, and the precise molecular contribution of its zinc finger domain remain open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No knockout or knockdown phenotype for TgSpt4 characterized","Direct binding of the complex to RNAPII (TgRpb1) not biochemically dissected in the timeline discoveries","No structural model of the TgSpt4-TgSpt5 complex"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["TgSpt4-TgSpt5 transcription elongation complex"],"partners":["TGSPT5","TGRPB1 (RNA POL II LARGEST SUBUNIT)"],"other_free_text":["Enrichment of the complex toward 3' ends of genes coincides with the P-Ser2 (Ser2-phosphorylated) elongating form of RNA Pol II [#1]","TgSpt4 and TgSpt5 complement yeast spt4/spt5 loss-of-function mutants, indicating functional conservation of the partnership [#0]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"30707945","id":"PMC_30707945","title":"Characterization of Toxoplasma gondii Spt5 like transcription elongation factor.","date":"2019","source":"Biochimica et biophysica acta. Gene regulatory mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/30707945","citation_count":11,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2922,"output_tokens":662,"usd":0.009348,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5371,"output_tokens":1674,"usd":0.034353,"stage2_stop_reason":"end_turn"},"total_usd":0.043701,"stage1_batch_id":"msgbatch_01TEPNZ4MCzJ7xtsNwosiDRk","stage2_batch_id":"msgbatch_01FQShM7n1sfCr4pWTDShmki","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"TgSpt4 (a small zinc finger protein) functions in conjunction with TgSpt5 as part of the transcription elongation complex in T. gondii, and together TgSpt4 and TgSpt5 can complement loss-of-function mutations in their yeast counterparts, establishing functional conservation of the Spt4-Spt5 partnership.\",\n      \"method\": \"Co-immunoprecipitation (TgSpt5–TgSpt4 interaction), yeast complementation assay\",\n      \"journal\": \"Biochimica et biophysica acta. Gene regulatory mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal interaction demonstrated and orthogonal yeast complementation assay validates function, single lab\",\n      \"pmids\": [\"30707945\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TgSpt4, as part of the TgSpt4-TgSpt5 complex, is required for transcription elongation; the complex associates with actively transcribed genes and its enrichment toward the 3' end of genes coincides with the P-Ser2 form of RNAPII, a marker of active elongation.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP) of TgSpt5; co-localization with P-Ser2 RNAPII\",\n      \"journal\": \"Biochimica et biophysica acta. Gene regulatory mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and co-localization data from single lab; TgSpt4 role inferred from its interaction partner TgSpt5's direct ChIP evidence\",\n      \"pmids\": [\"30707945\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"TgSpt4 is a small zinc finger protein that partners with TgSpt5 to form a transcription elongation factor complex in Toxoplasma gondii; this complex interacts with the largest subunit of RNA Pol II (TgRpb1), associates with actively transcribed genes enriched at their 3' ends, and is functionally conserved as demonstrated by complementation of yeast spt4/spt5 loss-of-function mutants.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TgSpt4 is a small zinc finger protein that acts as a transcription elongation factor in Toxoplasma gondii by partnering with TgSpt5 to form a heterodimeric complex analogous to the conserved Spt4-Spt5 elongation factor [#0]. The functional conservation of this partnership is established by the ability of TgSpt4 and TgSpt5 to complement loss-of-function mutations in their yeast counterparts [#0]. As part of this complex, TgSpt4 supports transcription elongation: the complex associates with actively transcribed genes, and its enrichment toward the 3' ends of genes coincides with the P-Ser2 elongating form of RNA polymerase II [#1]. Beyond this elongation-factor role defined in the single available study, no further mechanistic detail for TgSpt4 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Establishing whether T. gondii possesses a conserved Spt4-Spt5 elongation factor was needed to understand transcription regulation in this parasite; demonstrating physical partnership and cross-species functional rescue answered this.\",\n      \"evidence\": \"Co-immunoprecipitation showing TgSpt5-TgSpt4 interaction and yeast complementation of spt4/spt5 loss-of-function mutants\",\n      \"pmids\": [\"30707945\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Reciprocal interaction shown but the structural basis of the TgSpt4-TgSpt5 interface is undefined\",\n        \"Direct enzymatic or biochemical activity of TgSpt4 itself not assayed\",\n        \"Single lab, no independent replication\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Whether the TgSpt4-TgSpt5 complex acts on active transcription was unresolved; genome-wide localization coinciding with elongating polymerase established its role in transcription elongation.\",\n      \"evidence\": \"ChIP of TgSpt5 showing association with actively transcribed genes and 3'-end enrichment coinciding with P-Ser2 RNAPII\",\n      \"pmids\": [\"30707945\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"TgSpt4's specific contribution inferred from its partner TgSpt5's direct ChIP evidence rather than measured directly\",\n        \"Mechanism by which the complex is recruited to elongating polymerase not defined\",\n        \"Loss-of-function phenotype for TgSpt4 in the parasite not established\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TgSpt4 loss affects parasite viability, gene-specific transcription, and the precise molecular contribution of its zinc finger domain remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No knockout or knockdown phenotype for TgSpt4 characterized\",\n        \"Direct binding of the complex to RNAPII (TgRpb1) not biochemically dissected in the timeline discoveries\",\n        \"No structural model of the TgSpt4-TgSpt5 complex\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003712\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0000785\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006368\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"TgSpt4-TgSpt5 transcription elongation complex\"],\n    \"partners\": [\"TgSpt5\", \"TgRpb1 (RNA Pol II largest subunit)\"],\n    \"other_free_text\": [\n      \"Enrichment of the complex toward 3' ends of genes coincides with the P-Ser2 (Ser2-phosphorylated) elongating form of RNA Pol II [#1]\",\n      \"TgSpt4 and TgSpt5 complement yeast spt4/spt5 loss-of-function mutants, indicating functional conservation of the partnership [#0]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_261220","name":"SPT4","product":"transcription elongation factor SPT4","uniprot_acc":"A0A125YJM8","chromosome":"TGME49_chrVIIb","start_pos":1826184},{"strain":"GT1","gene_id":"TGGT1_261220","name":null,"product":"transcription elongation factor SPT4","uniprot_acc":null,"chromosome":"TGGT1_chrVIIb","start_pos":1799534},{"strain":"RH88","gene_id":"TGRH88_069390","name":null,"product":"transcription elongation factor SPT4","uniprot_acc":null,"chromosome":"CM023089","start_pos":1845143},{"strain":"VEG","gene_id":"TGVEG_261220","name":null,"product":"transcription elongation factor SPT4","uniprot_acc":"B9PKI4","chromosome":"TGVEG_chrVIIb","start_pos":1841680}]}