{"gene":"PF3D7_0506200","run_date":"2026-09-07T10:55:52","timeline":{"discoveries":[{"year":1993,"finding":"TBP (PF3D7_0506200) from P. falciparum is encoded by a single-copy gene on chromosome 5, expressed as a 1.8-kb mRNA encoding a 228-amino acid protein with a bipartite structure: a 45-aa species-specific N-terminal domain and a 183-aa C-terminal domain containing two directly repeated ~78-aa regions and a highly basic intervening region characteristic of TBPs. Most residues known to be involved in DNA binding are conserved despite only 42% sequence identity to yeast TBP.","method":"Gene isolation, sequencing, hydropathy analysis, and comparative sequence analysis","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gene characterization with sequence analysis and structural inference from primary sequence; single lab, no in vitro functional assay","pmids":["8444340"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"finding":"Recombinant GST-PfTBP (PF3D7_0506200) binds specifically to a consensus TATA box sequence (TATAA) located 81 bp upstream of the transcription start site in the kahrp promoter and to a TATA box-like sequence (TGTAA) at position -186 of the gbp-130 promoter, as demonstrated by supershift and DNase I footprinting assays. Chromatin immunoprecipitation confirmed that native PfTBP associates in vivo with both TATA box elements.","method":"Supershift assay, DNase I footprinting, chromatin immunoprecipitation (ChIP) with native protein","journal":"Molecular and biochemical parasitology","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — multiple orthogonal methods (supershift, footprinting, ChIP) in a single study demonstrating specific DNA binding in vitro and in vivo","pmids":["15760658"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2006,"finding":"A monoclonal antibody (MAb Pf.r1) specific to PfTBP (PF3D7_0506200) was generated and confirmed by Western blotting and immunofluorescence to recognize native PfTBP localized to the nuclei of P. falciparum parasites.","method":"Western blotting and immunofluorescence assay with monoclonal antibody on nuclear extracts","journal":"Hybridoma (2005)","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — nuclear localization confirmed by antibody-based methods, single lab, no functional consequence directly tested","pmids":["17203999"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"finding":"PfTBP (PF3D7_0506200) and PfTFIIE are bound to their cognate sequences at active and inactive erythrocytic-expressed gene promoters (including coding and 3' end regions), but not at promoters of non-erythrocytic-stage genes (csp and pfs25). PfTBP/PfTFIIE binding occurs independently of transcriptional activity and of histone H3/H4 acetylation, supporting a 'poised' preinitiation complex model.","method":"Chromatin immunoprecipitation (ChIP) across multiple stage-specific promoters in erythrocytic-stage parasites","journal":"Experimental parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP across multiple loci with functional interpretation; single lab, no in vitro reconstitution","pmids":["18951895"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2019,"finding":"Interaction proteomics of tagged proteins unveiled the composition of a TBP-associated-factor (TAF) complex in P. falciparum containing PfTBP (PF3D7_0506200), establishing its membership in this epigenetic complex.","method":"Tagging and quantitative interaction proteomics (mass spectrometry)","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mass spectrometry-based interaction proteomics with tagged bait; single study, complex composition defined but limited functional follow-up for TBP specifically","pmids":["31728527"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0506200 (TBP) is a nuclear TATA-binding protein in P. falciparum that directly binds consensus TATA box (TATAA) and TATA box-like (TGTAA) sequences in gene promoters both in vitro and in vivo, occupies promoters of all erythrocytic-stage-expressed genes in a 'poised' preinitiation complex independently of transcriptional activity and histone acetylation, and participates in a TBP-associated-factor (TAF) epigenetic complex."},"narrative":{"mechanistic_narrative":"PF3D7_0506200 (TBP) is the P. falciparum TATA-box-binding protein, a sequence-specific DNA-binding factor that nucleates RNA polymerase transcription preinitiation at gene promoters [PMID:15760658]. It is encoded by a single-copy chromosome 5 gene producing a 228-residue protein with the bipartite TBP architecture—a species-specific N-terminal region and a conserved C-terminal domain of two direct ~78-aa repeats flanking a basic core that retains most DNA-contacting residues despite only 42% identity to yeast TBP [PMID:8444340]. Recombinant PfTBP binds directly and specifically to a consensus TATA box (TATAA) and a TATA box-like element (TGTAA) upstream of the kahrp and gbp-130 transcription start sites, and native PfTBP associates with these elements in vivo [PMID:15760658]. PfTBP is a nuclear protein [PMID:17203999] that, together with PfTFIIE, occupies promoters of both active and inactive erythrocytic-stage genes—but not non-erythrocytic-stage promoters (csp, pfs25)—independently of transcriptional activity and histone H3/H4 acetylation, consistent with a constitutively poised preinitiation complex [PMID:18951895]. PfTBP is also a subunit of a P. falciparum TBP-associated-factor (TAF) complex [PMID:31728527]. Beyond its DNA-binding specificity, promoter occupancy, and complex membership, the mechanistic details of how PfTBP directs stage-specific transcription have not been characterized in the available corpus.","teleology":[{"year":1993,"claim":"Establishing whether P. falciparum encodes a bona fide TATA-binding protein was the first step in defining the parasite's basal transcription machinery; isolating the gene showed it exists as a single-copy locus with the conserved TBP fold.","evidence":"Gene isolation, sequencing, and comparative sequence/hydropathy analysis of a chromosome 5 locus","pmids":["8444340"],"confidence":"Medium","gaps":["DNA binding inferred from sequence conservation only, not tested functionally","N-terminal species-specific domain function unknown","no evidence of promoter recognition or partner interactions"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"claim":"Whether PfTBP actually recognizes parasite promoter elements was unresolved; direct binding assays demonstrated specific recognition of both consensus and TATA-like sequences in native gene promoters in vitro and in vivo.","evidence":"Supershift and DNase I footprinting with recombinant GST-PfTBP plus ChIP with native protein on kahrp and gbp-130 promoters","pmids":["15760658"],"confidence":"High","gaps":["does not establish requirement of PfTBP binding for transcription initiation","limited to two promoters","no structural model of the PfTBP-DNA complex"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2006,"claim":"Confirming the subcellular compartment where PfTBP acts was needed to place it in the transcription machinery; antibody-based detection localized native PfTBP to the parasite nucleus.","evidence":"Western blotting and immunofluorescence with a PfTBP-specific monoclonal antibody (Pf.r1) on nuclear extracts","pmids":["17203999"],"confidence":"Medium","gaps":["no functional consequence of localization tested","does not resolve dynamics across the erythrocytic cycle"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"claim":"It was unknown whether PfTBP occupancy tracks with active transcription or reflects a poised state; genome-region ChIP showed PfTBP and PfTFIIE occupy both active and inactive erythrocytic promoters independently of transcriptional activity and histone acetylation.","evidence":"ChIP for PfTBP and PfTFIIE across multiple stage-specific promoters, coding and 3' regions in erythrocytic-stage parasites","pmids":["18951895"],"confidence":"Medium","gaps":["mechanism maintaining the poised complex unresolved","no in vitro reconstitution of the preinitiation complex","does not explain how stage-specific transcription is triggered from poised promoters"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2019,"claim":"Whether PfTBP operates within a defined multiprotein assembly was addressed by interaction proteomics, which placed PfTBP as a subunit of a P. falciparum TBP-associated-factor (TAF) complex.","evidence":"Tagging and quantitative interaction proteomics (mass spectrometry) with tagged bait proteins","pmids":["31728527"],"confidence":"Medium","gaps":["functional role of PfTBP within the TAF complex not directly tested","no structural organization of the complex defined","individual TAF subunit contributions to PfTBP function unresolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"How PfTBP directs stage-specific and gene-specific transcription—the transition from poised preinitiation complexes to productive initiation and the roles of individual TAF partners—remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["no reconstitution of PfTBP-directed transcription initiation","no genetic loss-of-function analysis of PfTBP in the corpus","no structural model of PfTBP alone or in the TAF complex"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["TBP-associated-factor (TAF) complex [#4]"],"partners":["PFTFIIE (CO-OCCUPANCY AT PROMOTERS) [#3]"],"other_free_text":["Single-copy gene on chromosome 5 encoding a 228-aa protein with bipartite structure: species-specific N-terminal domain and conserved C-terminal domain with two direct ~78-aa repeats [#0]","Binds consensus TATA (TATAA) and TATA-like (TGTAA) elements upstream of kahrp and gbp-130 transcription start sites [#1]","Occupies active and inactive erythrocytic-stage promoters but not non-erythrocytic-stage promoters (csp, pfs25), independently of transcriptional activity and histone acetylation, consistent with a poised preinitiation complex [#3]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"1852174","id":"PMC_1852174","title":"The structure of the calmodulin gene of Plasmodium falciparum.","date":"1991","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/1852174","citation_count":75,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["TATA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"8444340","id":"PMC_8444340","title":"Characterisation of the gene encoding an unusually divergent TATA-binding protein (TBP) from the extremely A+T-rich human malaria parasite Plasmodium falciparum.","date":"1993","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/8444340","citation_count":66,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["TBP","TATA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"31728527","id":"PMC_31728527","title":"Epigenetic reader complexes of the human malaria parasite, Plasmodium falciparum.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/31728527","citation_count":48,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["TBP"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"8332491","id":"PMC_8332491","title":"Evolution of sequence repetition and gene duplications in the TATA-binding protein TBP (TFIID).","date":"1993","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/8332491","citation_count":35,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["TBP","TATA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"15760658","id":"PMC_15760658","title":"Recombinant and native Plasmodium falciparum TATA-binding-protein binds to a specific TATA box element in promoter regions.","date":"2005","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/15760658","citation_count":32,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["TATA-box binding protein","TATA-box-binding protein","TATA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18951895","id":"PMC_18951895","title":"Plasmodium falciparum: Preinitiation complex occupancy of active and inactive promoters during erythrocytic stage.","date":"2008","source":"Experimental parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/18951895","citation_count":25,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"31569300","id":"PMC_31569300","title":"The TATA-binding Protein DNA-binding domain of eukaryotic parasites is a potentially druggable target.","date":"2019","source":"Chemical biology & drug design","url":"https://pubmed.ncbi.nlm.nih.gov/31569300","citation_count":8,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["TBP","TATA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"15950069","id":"PMC_15950069","title":"Model of the TBP-TFIIB complex from Plasmodium falciparum: interface analysis and perspectives as a new target for antimalarial design.","date":"2005","source":"Archives of medical research","url":"https://pubmed.ncbi.nlm.nih.gov/15950069","citation_count":7,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["TBP"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"17203999","id":"PMC_17203999","title":"Preparation and characterization of a monoclonal antibody specific to Plasmodium falciparum TATA binding protein.","date":"2006","source":"Hybridoma (2005)","url":"https://pubmed.ncbi.nlm.nih.gov/17203999","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["TBP","TATA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38030676","id":"PMC_38030676","title":"Evaluating the stability of host-reference gene expression and simultaneously quantifying parasite burden and host immune responses in murine malaria.","date":"2023","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/38030676","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["TBP","TATA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7303,"output_tokens":1484,"usd":0.022084,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6440,"output_tokens":2800,"usd":0.0511,"stage2_stop_reason":"end_turn"},"total_usd":0.073184,"stage1_batch_id":"msgbatch_01DbiymDmubkPpYvdbAu5a7V","stage2_batch_id":"msgbatch_012TbrWvMRH129T7PQ4SmvrJ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1993,\n      \"finding\": \"TBP (PF3D7_0506200) from P. falciparum is encoded by a single-copy gene on chromosome 5, expressed as a 1.8-kb mRNA encoding a 228-amino acid protein with a bipartite structure: a 45-aa species-specific N-terminal domain and a 183-aa C-terminal domain containing two directly repeated ~78-aa regions and a highly basic intervening region characteristic of TBPs. Most residues known to be involved in DNA binding are conserved despite only 42% sequence identity to yeast TBP.\",\n      \"method\": \"Gene isolation, sequencing, hydropathy analysis, and comparative sequence analysis\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gene characterization with sequence analysis and structural inference from primary sequence; single lab, no in vitro functional assay\",\n      \"pmids\": [\"8444340\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Recombinant GST-PfTBP (PF3D7_0506200) binds specifically to a consensus TATA box sequence (TATAA) located 81 bp upstream of the transcription start site in the kahrp promoter and to a TATA box-like sequence (TGTAA) at position -186 of the gbp-130 promoter, as demonstrated by supershift and DNase I footprinting assays. Chromatin immunoprecipitation confirmed that native PfTBP associates in vivo with both TATA box elements.\",\n      \"method\": \"Supershift assay, DNase I footprinting, chromatin immunoprecipitation (ChIP) with native protein\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — multiple orthogonal methods (supershift, footprinting, ChIP) in a single study demonstrating specific DNA binding in vitro and in vivo\",\n      \"pmids\": [\"15760658\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"A monoclonal antibody (MAb Pf.r1) specific to PfTBP (PF3D7_0506200) was generated and confirmed by Western blotting and immunofluorescence to recognize native PfTBP localized to the nuclei of P. falciparum parasites.\",\n      \"method\": \"Western blotting and immunofluorescence assay with monoclonal antibody on nuclear extracts\",\n      \"journal\": \"Hybridoma (2005)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — nuclear localization confirmed by antibody-based methods, single lab, no functional consequence directly tested\",\n      \"pmids\": [\"17203999\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"PfTBP (PF3D7_0506200) and PfTFIIE are bound to their cognate sequences at active and inactive erythrocytic-expressed gene promoters (including coding and 3' end regions), but not at promoters of non-erythrocytic-stage genes (csp and pfs25). PfTBP/PfTFIIE binding occurs independently of transcriptional activity and of histone H3/H4 acetylation, supporting a 'poised' preinitiation complex model.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP) across multiple stage-specific promoters in erythrocytic-stage parasites\",\n      \"journal\": \"Experimental parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP across multiple loci with functional interpretation; single lab, no in vitro reconstitution\",\n      \"pmids\": [\"18951895\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Interaction proteomics of tagged proteins unveiled the composition of a TBP-associated-factor (TAF) complex in P. falciparum containing PfTBP (PF3D7_0506200), establishing its membership in this epigenetic complex.\",\n      \"method\": \"Tagging and quantitative interaction proteomics (mass spectrometry)\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mass spectrometry-based interaction proteomics with tagged bait; single study, complex composition defined but limited functional follow-up for TBP specifically\",\n      \"pmids\": [\"31728527\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0506200 (TBP) is a nuclear TATA-binding protein in P. falciparum that directly binds consensus TATA box (TATAA) and TATA box-like (TGTAA) sequences in gene promoters both in vitro and in vivo, occupies promoters of all erythrocytic-stage-expressed genes in a 'poised' preinitiation complex independently of transcriptional activity and histone acetylation, and participates in a TBP-associated-factor (TAF) epigenetic complex.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0506200 (TBP) is the P. falciparum TATA-box-binding protein, a sequence-specific DNA-binding factor that nucleates RNA polymerase transcription preinitiation at gene promoters [#1]. It is encoded by a single-copy chromosome 5 gene producing a 228-residue protein with the bipartite TBP architecture—a species-specific N-terminal region and a conserved C-terminal domain of two direct ~78-aa repeats flanking a basic core that retains most DNA-contacting residues despite only 42% identity to yeast TBP [#0]. Recombinant PfTBP binds directly and specifically to a consensus TATA box (TATAA) and a TATA box-like element (TGTAA) upstream of the kahrp and gbp-130 transcription start sites, and native PfTBP associates with these elements in vivo [#1]. PfTBP is a nuclear protein [#2] that, together with PfTFIIE, occupies promoters of both active and inactive erythrocytic-stage genes—but not non-erythrocytic-stage promoters (csp, pfs25)—independently of transcriptional activity and histone H3/H4 acetylation, consistent with a constitutively poised preinitiation complex [#3]. PfTBP is also a subunit of a P. falciparum TBP-associated-factor (TAF) complex [#4]. Beyond its DNA-binding specificity, promoter occupancy, and complex membership, the mechanistic details of how PfTBP directs stage-specific transcription have not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 1993,\n      \"claim\": \"Establishing whether P. falciparum encodes a bona fide TATA-binding protein was the first step in defining the parasite's basal transcription machinery; isolating the gene showed it exists as a single-copy locus with the conserved TBP fold.\",\n      \"evidence\": \"Gene isolation, sequencing, and comparative sequence/hydropathy analysis of a chromosome 5 locus\",\n      \"pmids\": [\"8444340\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"DNA binding inferred from sequence conservation only, not tested functionally\",\n        \"N-terminal species-specific domain function unknown\",\n        \"no evidence of promoter recognition or partner interactions\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Whether PfTBP actually recognizes parasite promoter elements was unresolved; direct binding assays demonstrated specific recognition of both consensus and TATA-like sequences in native gene promoters in vitro and in vivo.\",\n      \"evidence\": \"Supershift and DNase I footprinting with recombinant GST-PfTBP plus ChIP with native protein on kahrp and gbp-130 promoters\",\n      \"pmids\": [\"15760658\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"does not establish requirement of PfTBP binding for transcription initiation\",\n        \"limited to two promoters\",\n        \"no structural model of the PfTBP-DNA complex\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Confirming the subcellular compartment where PfTBP acts was needed to place it in the transcription machinery; antibody-based detection localized native PfTBP to the parasite nucleus.\",\n      \"evidence\": \"Western blotting and immunofluorescence with a PfTBP-specific monoclonal antibody (Pf.r1) on nuclear extracts\",\n      \"pmids\": [\"17203999\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"no functional consequence of localization tested\",\n        \"does not resolve dynamics across the erythrocytic cycle\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"It was unknown whether PfTBP occupancy tracks with active transcription or reflects a poised state; genome-region ChIP showed PfTBP and PfTFIIE occupy both active and inactive erythrocytic promoters independently of transcriptional activity and histone acetylation.\",\n      \"evidence\": \"ChIP for PfTBP and PfTFIIE across multiple stage-specific promoters, coding and 3' regions in erythrocytic-stage parasites\",\n      \"pmids\": [\"18951895\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"mechanism maintaining the poised complex unresolved\",\n        \"no in vitro reconstitution of the preinitiation complex\",\n        \"does not explain how stage-specific transcription is triggered from poised promoters\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Whether PfTBP operates within a defined multiprotein assembly was addressed by interaction proteomics, which placed PfTBP as a subunit of a P. falciparum TBP-associated-factor (TAF) complex.\",\n      \"evidence\": \"Tagging and quantitative interaction proteomics (mass spectrometry) with tagged bait proteins\",\n      \"pmids\": [\"31728527\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"functional role of PfTBP within the TAF complex not directly tested\",\n        \"no structural organization of the complex defined\",\n        \"individual TAF subunit contributions to PfTBP function unresolved\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PfTBP directs stage-specific and gene-specific transcription—the transition from poised preinitiation complexes to productive initiation and the roles of individual TAF partners—remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"no reconstitution of PfTBP-directed transcription initiation\",\n        \"no genetic loss-of-function analysis of PfTBP in the corpus\",\n        \"no structural model of PfTBP alone or in the TAF complex\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003700\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0000976\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0001091\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0000785\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006367\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0006355\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"complexes\": [\n      \"TBP-associated-factor (TAF) complex [#4]\"\n    ],\n    \"partners\": [\n      \"PfTFIIE (co-occupancy at promoters) [#3]\"\n    ],\n    \"other_free_text\": [\n      \"Single-copy gene on chromosome 5 encoding a 228-aa protein with bipartite structure: species-specific N-terminal domain and conserved C-terminal domain with two direct ~78-aa repeats [#0]\",\n      \"Binds consensus TATA (TATAA) and TATA-like (TGTAA) elements upstream of kahrp and gbp-130 transcription start sites [#1]\",\n      \"Occupies active and inactive erythrocytic-stage promoters but not non-erythrocytic-stage promoters (csp, pfs25), independently of transcriptional activity and histone acetylation, consistent with a poised preinitiation complex [#3]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0506200","name":null,"product":"TATA-box-binding protein","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1105800","name":null,"product":"TATA-box binding protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1027400","name":null,"product":"TATA-box-binding protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"TBP","evaluation":null}