{"gene":"TG_233000","gene_symbol":"SPT5","run_date":"2026-09-08T12:58:24","timeline":{"discoveries":[{"year":2019,"finding":"TgSpt5 functions in conjunction with a small zinc finger protein TgSpt4, forming a functional complex involved in transcription elongation in T. gondii.","method":"Co-immunoprecipitation / functional interaction studies","journal":"Biochimica et biophysica acta. Gene regulatory mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — interaction demonstrated alongside multiple functional assays in a single lab study","pmids":["30707945"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"TgSpt5 physically interacts with TgRpb1, the largest subunit of RNA polymerase II, linking it directly to the transcription elongation machinery.","method":"Co-immunoprecipitation / pulldown","journal":"Biochimica et biophysica acta. Gene regulatory mechanisms","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP result supported by chromatin occupancy data in the same study","pmids":["30707945"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"TgSpt5 associates with actively transcribed genes and is enriched towards the 3' end of genes, coinciding with the P-Ser2 form of RNAPII (a marker of active elongation), establishing its role in transcription elongation in vivo.","method":"Chromatin immunoprecipitation (ChIP)","journal":"Biochimica et biophysica acta. Gene regulatory mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP occupancy data with multiple gene targets in a single lab study","pmids":["30707945"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"TgSpt5 is phosphorylated by the T. gondii Cdk9 homolog TgCrk9, and inhibition of TgCrk9 results in loss of TgSpt5 enrichment at 3' gene sites and a repressive effect on parasite progression, indicating that TgCrk9-mediated phosphorylation is required for TgSpt5 function.","method":"Kinase inhibition assay combined with ChIP and parasite growth assays","journal":"Biochimica et biophysica acta. Gene regulatory mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — phosphorylation and functional consequence demonstrated by multiple orthogonal methods (inhibition, ChIP, growth phenotype) in a single lab study","pmids":["30707945"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"TgSpt5 together with TgSpt4 can complement loss-of-function mutations in the yeast Spt4/Spt5 counterparts, demonstrating functional conservation of the T. gondii complex.","method":"Yeast complementation assay","journal":"Biochimica et biophysica acta. Gene regulatory mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic complementation in a well-established heterologous system, single lab study","pmids":["30707945"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"TgSpt5 is a transcription elongation factor in Toxoplasma gondii that forms a complex with TgSpt4, physically interacts with the RNAPII largest subunit TgRpb1, is enriched at the 3' ends of actively transcribed genes coincident with elongation-associated P-Ser2 RNAPII, and is phosphorylated by the Cdk9 homolog TgCrk9, which is required for its chromatin association and proper elongation function."},"narrative":{"mechanistic_narrative":"TgSpt5 is a transcription elongation factor in Toxoplasma gondii that couples RNA polymerase II to productive elongation [PMID:30707945]. It forms a functional complex with the small zinc-finger protein TgSpt4 [PMID:30707945] and physically associates with TgRpb1, the largest subunit of RNAPII, directly linking it to the elongation machinery [PMID:30707945]. By chromatin immunoprecipitation, TgSpt5 occupies actively transcribed genes and is enriched toward their 3' ends, coincident with the elongation-associated P-Ser2 form of RNAPII [PMID:30707945]. Its chromatin engagement is controlled by phosphorylation: the Cdk9 homolog TgCrk9 phosphorylates TgSpt5, and TgCrk9 inhibition abolishes TgSpt5 enrichment at 3' gene sites and impairs parasite progression [PMID:30707945]. The functional conservation of this activity is demonstrated by the ability of TgSpt5/TgSpt4 to complement loss of the yeast Spt4/Spt5 counterparts [PMID:30707945].","teleology":[{"year":2019,"claim":"Establishing whether Toxoplasma possesses a conserved Spt4/Spt5 elongation module addressed whether the parasite uses the canonical eukaryotic elongation apparatus; the finding defined TgSpt5 as part of a functional complex with the zinc-finger protein TgSpt4.","evidence":"Co-immunoprecipitation and functional interaction studies in T. gondii, with yeast complementation confirming conservation","pmids":["30707945"],"confidence":"Medium","gaps":["Stoichiometry and structural architecture of the TgSpt4/TgSpt5 complex not resolved","Whether the complex has additional parasite-specific subunits unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"Determining how TgSpt5 connects to the transcription machinery showed it physically interacts with the RNAPII largest subunit TgRpb1, placing it directly on elongating polymerase.","evidence":"Co-immunoprecipitation/pulldown in T. gondii","pmids":["30707945"],"confidence":"Medium","gaps":["Interaction from single Co-IP without reciprocal validation","Interface/domains mediating the TgRpb1 contact not mapped"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"Mapping where TgSpt5 acts on genes established it as an in vivo elongation factor: it occupies actively transcribed genes and is enriched at 3' ends coincident with P-Ser2 RNAPII.","evidence":"Chromatin immunoprecipitation across multiple gene targets in T. gondii","pmids":["30707945"],"confidence":"Medium","gaps":["Genome-wide occupancy profile not established","Direct effect on elongation rate or processivity not measured"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"Identifying the regulatory input to TgSpt5 showed that the Cdk9 homolog TgCrk9 phosphorylates it, and this phosphorylation is required for TgSpt5 chromatin association and parasite growth.","evidence":"TgCrk9 kinase inhibition combined with ChIP and parasite growth assays in T. gondii","pmids":["30707945"],"confidence":"Medium","gaps":["Specific phosphosites on TgSpt5 not identified","Whether TgCrk9 acts directly versus through an intermediate not fully distinguished"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"How TgSpt5 phosphorylation state mechanistically couples to elongation rate, RNAPII pausing/release, and the broader parasite gene-expression program remains open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the TgSpt4/TgSpt5-RNAPII assembly","Direct measurement of elongation kinetics upon TgSpt5 depletion lacking","Genome-wide targets and phosphosite-specific consequences uncharacterized"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["TgSpt4/TgSpt5 elongation complex"],"partners":["TGSPT4","TGRPB1 (RNAPII LARGEST SUBUNIT)","TGCRK9 (CDK9 HOMOLOG KINASE)"],"other_free_text":["TgSpt5 enrichment at 3' gene ends coincides with the P-Ser2 (elongation-associated) form of RNAPII.","TgCrk9-mediated phosphorylation of TgSpt5 is required for its chromatin association and for parasite progression.","TgSpt5/TgSpt4 functionally complement yeast Spt4/Spt5 loss-of-function, indicating conservation of elongation function."]},"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":1180,"usd":0.013233,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6165,"output_tokens":2251,"usd":0.04355,"stage2_stop_reason":"end_turn"},"total_usd":0.056783,"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\": \"TgSpt5 functions in conjunction with a small zinc finger protein TgSpt4, forming a functional complex involved in transcription elongation in T. gondii.\",\n      \"method\": \"Co-immunoprecipitation / functional interaction studies\",\n      \"journal\": \"Biochimica et biophysica acta. Gene regulatory mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — interaction demonstrated alongside multiple functional assays in a single lab study\",\n      \"pmids\": [\"30707945\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TgSpt5 physically interacts with TgRpb1, the largest subunit of RNA polymerase II, linking it directly to the transcription elongation machinery.\",\n      \"method\": \"Co-immunoprecipitation / pulldown\",\n      \"journal\": \"Biochimica et biophysica acta. Gene regulatory mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP result supported by chromatin occupancy data in the same study\",\n      \"pmids\": [\"30707945\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TgSpt5 associates with actively transcribed genes and is enriched towards the 3' end of genes, coinciding with the P-Ser2 form of RNAPII (a marker of active elongation), establishing its role in transcription elongation in vivo.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP)\",\n      \"journal\": \"Biochimica et biophysica acta. Gene regulatory mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP occupancy data with multiple gene targets in a single lab study\",\n      \"pmids\": [\"30707945\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TgSpt5 is phosphorylated by the T. gondii Cdk9 homolog TgCrk9, and inhibition of TgCrk9 results in loss of TgSpt5 enrichment at 3' gene sites and a repressive effect on parasite progression, indicating that TgCrk9-mediated phosphorylation is required for TgSpt5 function.\",\n      \"method\": \"Kinase inhibition assay combined with ChIP and parasite growth assays\",\n      \"journal\": \"Biochimica et biophysica acta. Gene regulatory mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — phosphorylation and functional consequence demonstrated by multiple orthogonal methods (inhibition, ChIP, growth phenotype) in a single lab study\",\n      \"pmids\": [\"30707945\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TgSpt5 together with TgSpt4 can complement loss-of-function mutations in the yeast Spt4/Spt5 counterparts, demonstrating functional conservation of the T. gondii complex.\",\n      \"method\": \"Yeast complementation assay\",\n      \"journal\": \"Biochimica et biophysica acta. Gene regulatory mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic complementation in a well-established heterologous system, single lab study\",\n      \"pmids\": [\"30707945\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"TgSpt5 is a transcription elongation factor in Toxoplasma gondii that forms a complex with TgSpt4, physically interacts with the RNAPII largest subunit TgRpb1, is enriched at the 3' ends of actively transcribed genes coincident with elongation-associated P-Ser2 RNAPII, and is phosphorylated by the Cdk9 homolog TgCrk9, which is required for its chromatin association and proper elongation function.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TgSpt5 is a transcription elongation factor in Toxoplasma gondii that couples RNA polymerase II to productive elongation [#2]. It forms a functional complex with the small zinc-finger protein TgSpt4 [#0] and physically associates with TgRpb1, the largest subunit of RNAPII, directly linking it to the elongation machinery [#1]. By chromatin immunoprecipitation, TgSpt5 occupies actively transcribed genes and is enriched toward their 3' ends, coincident with the elongation-associated P-Ser2 form of RNAPII [#2]. Its chromatin engagement is controlled by phosphorylation: the Cdk9 homolog TgCrk9 phosphorylates TgSpt5, and TgCrk9 inhibition abolishes TgSpt5 enrichment at 3' gene sites and impairs parasite progression [#3]. The functional conservation of this activity is demonstrated by the ability of TgSpt5/TgSpt4 to complement loss of the yeast Spt4/Spt5 counterparts [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Establishing whether Toxoplasma possesses a conserved Spt4/Spt5 elongation module addressed whether the parasite uses the canonical eukaryotic elongation apparatus; the finding defined TgSpt5 as part of a functional complex with the zinc-finger protein TgSpt4.\",\n      \"evidence\": \"Co-immunoprecipitation and functional interaction studies in T. gondii, with yeast complementation confirming conservation\",\n      \"pmids\": [\"30707945\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"single lab study\",\n      \"gaps\": [\"Stoichiometry and structural architecture of the TgSpt4/TgSpt5 complex not resolved\", \"Whether the complex has additional parasite-specific subunits unknown\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Determining how TgSpt5 connects to the transcription machinery showed it physically interacts with the RNAPII largest subunit TgRpb1, placing it directly on elongating polymerase.\",\n      \"evidence\": \"Co-immunoprecipitation/pulldown in T. gondii\",\n      \"pmids\": [\"30707945\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interaction from single Co-IP without reciprocal validation\", \"Interface/domains mediating the TgRpb1 contact not mapped\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Mapping where TgSpt5 acts on genes established it as an in vivo elongation factor: it occupies actively transcribed genes and is enriched at 3' ends coincident with P-Ser2 RNAPII.\",\n      \"evidence\": \"Chromatin immunoprecipitation across multiple gene targets in T. gondii\",\n      \"pmids\": [\"30707945\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Genome-wide occupancy profile not established\", \"Direct effect on elongation rate or processivity not measured\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identifying the regulatory input to TgSpt5 showed that the Cdk9 homolog TgCrk9 phosphorylates it, and this phosphorylation is required for TgSpt5 chromatin association and parasite growth.\",\n      \"evidence\": \"TgCrk9 kinase inhibition combined with ChIP and parasite growth assays in T. gondii\",\n      \"pmids\": [\"30707945\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific phosphosites on TgSpt5 not identified\", \"Whether TgCrk9 acts directly versus through an intermediate not fully distinguished\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TgSpt5 phosphorylation state mechanistically couples to elongation rate, RNAPII pausing/release, and the broader parasite gene-expression program remains open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of the TgSpt4/TgSpt5-RNAPII assembly\", \"Direct measurement of elongation kinetics upon TgSpt5 depletion lacking\", \"Genome-wide targets and phosphosite-specific consequences uncharacterized\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003711\", \"supporting_discovery_ids\": [0, 2, 4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0070063\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0000785\", \"supporting_discovery_ids\": [2, 3], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006368\", \"supporting_discovery_ids\": [2, 3], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"TgSpt4/TgSpt5 elongation complex\"],\n    \"partners\": [\"TgSpt4\", \"TgRpb1 (RNAPII largest subunit)\", \"TgCrk9 (Cdk9 homolog kinase)\"],\n    \"other_free_text\": [\n      \"TgSpt5 enrichment at 3' gene ends coincides with the P-Ser2 (elongation-associated) form of RNAPII.\",\n      \"TgCrk9-mediated phosphorylation of TgSpt5 is required for its chromatin association and for parasite progression.\",\n      \"TgSpt5/TgSpt4 functionally complement yeast Spt4/Spt5 loss-of-function, indicating conservation of elongation function.\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_233000","name":"SPT5","product":"KOW motif domain-containing protein","uniprot_acc":"S8GAM4","chromosome":"TGME49_chrVIII","start_pos":2317668},{"strain":"GT1","gene_id":"TGGT1_233000","name":null,"product":"KOW motif domain-containing protein","uniprot_acc":null,"chromosome":"TGGT1_chrVIII","start_pos":2313902},{"strain":"RH88","gene_id":"TGRH88_076980","name":null,"product":"KOW motif domain-containing protein","uniprot_acc":null,"chromosome":"CM023089","start_pos":7424177},{"strain":"VEG","gene_id":"TGVEG_233000","name":null,"product":"KOW motif domain-containing protein","uniprot_acc":"V5BL66","chromosome":"TGVEG_chrVIII","start_pos":2327067}]}