{"gene":"PF3D7_1234100","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2019,"finding":"BDP5 (PF3D7_1234100) was identified as a component of the TAF (TBP-associated-factor) epigenetic reader complex in P. falciparum, revealed by tagging and interaction proteomics (quantitative proteomic approaches including histone peptide pull-downs and co-immunoprecipitation/interaction proteomics of tagged proteins).","method":"Quantitative interaction proteomics (histone peptide pull-downs, tagging and co-immunoprecipitation of tagged proteins, mass spectrometry)","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal interaction proteomics in a single lab with multiple orthogonal methods (pull-down + tagging + MS), but BDP5 itself is not the primary focus and its specific contribution within the complex is not functionally dissected","pmids":["31728527"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"finding":"BDP5 (PF3D7_1234100, also referred to as TAF1/BDP5 in the abstract) is phosphorylated at multiple residues (T2289, S2291, S2395, T2397) in schizont-stage parasites, and these phosphorylation levels are upregulated upon knockdown of the phosphatase PfNIF4, indicating that PfNIF4 dephosphorylates BDP5 as part of its regulation of the TAF1/BDP5 complex.","method":"Quantitative phosphoproteomic profiling (TurboID-based proximity proteomics and phosphoproteomics) following inducible ribozyme-mediated knockdown of PfNIF4","journal":"mBio","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single phosphoproteomic dataset; BDP5 phosphorylation is identified as a downstream readout of PfNIF4 KD but no direct enzymatic assay or mutagenesis of BDP5 itself was performed","pmids":["35938722"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"BDP5 (PF3D7_1234100) shows stage-specific chromatin binding in P. falciparum: DiBioCUT&Tag profiling of BDP5-FKBP/FRB-TurboID dimers at trophozoites (24–32 hpi) and schizonts (32–40 hpi) revealed distinct peak profiles with enrichment of the DiBioCUT&Tag signal upstream of ATG in a stage-specific manner, consistent with BDP5 binding open/active chromatin regions in a stage-dependent fashion.","method":"DiBioCUT&Tag (dimerization-induced proximity labeling followed by CUT&Tag) on FKBP-tagged BDP5 parasites with rapalog-inducible FRB-TurboID; bioinformatic peak analysis","journal":"Cell reports methods","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, novel method whose background signal could not be fully disentangled from true BDP5 signal in open chromatin; the authors explicitly note the result is confounded by free-floating miniTurbo background, making the BDP5-specific signal uninterpretable","pmids":["40675147"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"BDP5 (PF3D7_1234100) is a bromodomain-containing protein in P. falciparum that resides in the TAF (TBP-associated-factor) epigenetic reader complex, is phosphorylated at multiple residues in schizonts in a manner regulated by the phosphatase PfNIF4, and appears to associate with open/active chromatin regions in a stage-specific manner, but its specific molecular function within the TAF complex and the functional consequences of its phosphorylation remain uncharacterized."},"narrative":{"mechanistic_narrative":"BDP5 (PF3D7_1234100) is a bromodomain-containing protein of Plasmodium falciparum that functions as a subunit of the TAF (TBP-associated-factor) epigenetic reader complex, identified through histone peptide pull-downs and interaction proteomics of tagged proteins [PMID:31728527]. Beyond its membership in this complex, BDP5's specific molecular contribution has not been dissected in the available corpus. In schizont-stage parasites BDP5 is phosphorylated at multiple residues (T2289, S2291, S2395, T2397), and these phosphosites accumulate upon knockdown of the phosphatase PfNIF4, placing BDP5 as a substrate whose phosphorylation state is regulated by PfNIF4 [PMID:35938722]. Stage-specific chromatin-binding profiling is consistent with BDP5 associating with chromatin in a stage-dependent manner, though the authors note this signal could not be cleanly separated from assay background [PMID:40675147]. The functional consequences of BDP5 phosphorylation and its precise role within the TAF complex remain uncharacterized in the available corpus.","teleology":[{"year":2019,"claim":"Establishing which epigenetic machinery BDP5 belongs to was the first step in placing this bromodomain protein in a functional context; interaction proteomics assigned it to the TAF reader complex.","evidence":"Histone peptide pull-downs, tagging and co-immunoprecipitation of tagged proteins with mass spectrometry in P. falciparum","pmids":["31728527"],"confidence":"Medium","gaps":["BDP5's specific molecular contribution within the TAF complex was not dissected","No structural or domain-level characterization of BDP5's interactions","No functional knockout/knockdown phenotype for BDP5 reported"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"claim":"Whether BDP5 activity is post-translationally regulated was addressed by mapping its phosphosites and linking them to a phosphatase, establishing BDP5 as a PfNIF4-regulated substrate in schizonts.","evidence":"TurboID proximity phosphoproteomics following inducible ribozyme knockdown of PfNIF4 in P. falciparum","pmids":["35938722"],"confidence":"Low","gaps":["No direct enzymatic assay or mutagenesis of BDP5 phosphosites was performed","Functional consequence of BDP5 phosphorylation is unknown","Whether PfNIF4 acts directly on BDP5 versus indirectly is not established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Where BDP5 acts on the genome across the cell cycle was probed by proximity-based chromatin profiling, indicating stage-specific association with open/active chromatin regions.","evidence":"DiBioCUT&Tag on FKBP-tagged BDP5 with rapalog-inducible FRB-TurboID at trophozoite and schizont stages in P. falciparum","pmids":["40675147"],"confidence":"Low","gaps":["BDP5-specific signal was confounded by free-floating miniTurbo background, making it uninterpretable per the authors","No validated target genes or loci identified","No link between chromatin binding and transcriptional output"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The specific molecular function of BDP5 within the TAF complex, the histone marks its bromodomain reads, and the functional consequences of its PfNIF4-regulated phosphorylation remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No demonstrated bromodomain ligand or histone-mark specificity for BDP5","No loss-of-function phenotype attributing a biological role to BDP5","No causal link between phosphorylation state and chromatin binding or complex function"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["TAF (TBP-associated-factor) epigenetic reader complex [#0]"],"partners":["PFNIF4 PHOSPHATASE (REGULATES BDP5 PHOSPHORYLATION) [#1]"],"other_free_text":["Phosphorylated at T2289, S2291, S2395, T2397 in schizonts; phosphosites accumulate upon PfNIF4 knockdown [#1]","Stage-specific chromatin association reported by DiBioCUT&Tag, but confounded by assay background [#2]","Bromodomain-containing protein; no ligand/histone-mark specificity established in the corpus"]}},"prefetch_data":{},"corpus_meta":[{"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":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40675147","id":"","title":"CUT&Tag and DiBioCUT&Tag enable investigation of the AT-rich epigenome of Plasmodium falciparum from low-input samples.","date":"2025","source":"Cell reports methods","url":"https://pubmed.ncbi.nlm.nih.gov/40675147","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["BDP5"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39639029","id":"","title":"Population genomics and transcriptomics of Plasmodium falciparum in Cambodia and Vietnam uncover key components of the artemisinin resistance genetic background.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/39639029","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["BDP5"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35493110","id":"","title":"The Putative Bromodomain Protein PfBDP7 of the Human Malaria Parasite Plasmodium Falciparum Cooperates With PfBDP1 in the Silencing of Variant Surface Antigen Expression.","date":"2022","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/35493110","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["BDP5"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35938722","id":"","title":"The Plasmodium falciparum Nuclear Protein Phosphatase NIF4 Is Required for Efficient Merozoite Invasion and Regulates Artemisinin Sensitivity.","date":"2022","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/35938722","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["BDP5"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8606,"output_tokens":1142,"usd":0.021474,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5934,"output_tokens":1864,"usd":0.038135,"stage2_stop_reason":"end_turn"},"total_usd":0.059609,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"BDP5 (PF3D7_1234100) was identified as a component of the TAF (TBP-associated-factor) epigenetic reader complex in P. falciparum, revealed by tagging and interaction proteomics (quantitative proteomic approaches including histone peptide pull-downs and co-immunoprecipitation/interaction proteomics of tagged proteins).\",\n      \"method\": \"Quantitative interaction proteomics (histone peptide pull-downs, tagging and co-immunoprecipitation of tagged proteins, mass spectrometry)\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal interaction proteomics in a single lab with multiple orthogonal methods (pull-down + tagging + MS), but BDP5 itself is not the primary focus and its specific contribution within the complex is not functionally dissected\",\n      \"pmids\": [\"31728527\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"BDP5 (PF3D7_1234100, also referred to as TAF1/BDP5 in the abstract) is phosphorylated at multiple residues (T2289, S2291, S2395, T2397) in schizont-stage parasites, and these phosphorylation levels are upregulated upon knockdown of the phosphatase PfNIF4, indicating that PfNIF4 dephosphorylates BDP5 as part of its regulation of the TAF1/BDP5 complex.\",\n      \"method\": \"Quantitative phosphoproteomic profiling (TurboID-based proximity proteomics and phosphoproteomics) following inducible ribozyme-mediated knockdown of PfNIF4\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single phosphoproteomic dataset; BDP5 phosphorylation is identified as a downstream readout of PfNIF4 KD but no direct enzymatic assay or mutagenesis of BDP5 itself was performed\",\n      \"pmids\": [\"35938722\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"BDP5 (PF3D7_1234100) shows stage-specific chromatin binding in P. falciparum: DiBioCUT&Tag profiling of BDP5-FKBP/FRB-TurboID dimers at trophozoites (24–32 hpi) and schizonts (32–40 hpi) revealed distinct peak profiles with enrichment of the DiBioCUT&Tag signal upstream of ATG in a stage-specific manner, consistent with BDP5 binding open/active chromatin regions in a stage-dependent fashion.\",\n      \"method\": \"DiBioCUT&Tag (dimerization-induced proximity labeling followed by CUT&Tag) on FKBP-tagged BDP5 parasites with rapalog-inducible FRB-TurboID; bioinformatic peak analysis\",\n      \"journal\": \"Cell reports methods\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, novel method whose background signal could not be fully disentangled from true BDP5 signal in open chromatin; the authors explicitly note the result is confounded by free-floating miniTurbo background, making the BDP5-specific signal uninterpretable\",\n      \"pmids\": [\"40675147\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"BDP5 (PF3D7_1234100) is a bromodomain-containing protein in P. falciparum that resides in the TAF (TBP-associated-factor) epigenetic reader complex, is phosphorylated at multiple residues in schizonts in a manner regulated by the phosphatase PfNIF4, and appears to associate with open/active chromatin regions in a stage-specific manner, but its specific molecular function within the TAF complex and the functional consequences of its phosphorylation remain uncharacterized.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"BDP5 (PF3D7_1234100) is a bromodomain-containing protein of Plasmodium falciparum that functions as a subunit of the TAF (TBP-associated-factor) epigenetic reader complex, identified through histone peptide pull-downs and interaction proteomics of tagged proteins [#0]. Beyond its membership in this complex, BDP5's specific molecular contribution has not been dissected in the available corpus. In schizont-stage parasites BDP5 is phosphorylated at multiple residues (T2289, S2291, S2395, T2397), and these phosphosites accumulate upon knockdown of the phosphatase PfNIF4, placing BDP5 as a substrate whose phosphorylation state is regulated by PfNIF4 [#1]. Stage-specific chromatin-binding profiling is consistent with BDP5 associating with chromatin in a stage-dependent manner, though the authors note this signal could not be cleanly separated from assay background [#2]. The functional consequences of BDP5 phosphorylation and its precise role within the TAF complex remain uncharacterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Establishing which epigenetic machinery BDP5 belongs to was the first step in placing this bromodomain protein in a functional context; interaction proteomics assigned it to the TAF reader complex.\",\n      \"evidence\": \"Histone peptide pull-downs, tagging and co-immunoprecipitation of tagged proteins with mass spectrometry in P. falciparum\",\n      \"pmids\": [\"31728527\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"BDP5's specific molecular contribution within the TAF complex was not dissected\",\n        \"No structural or domain-level characterization of BDP5's interactions\",\n        \"No functional knockout/knockdown phenotype for BDP5 reported\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Whether BDP5 activity is post-translationally regulated was addressed by mapping its phosphosites and linking them to a phosphatase, establishing BDP5 as a PfNIF4-regulated substrate in schizonts.\",\n      \"evidence\": \"TurboID proximity phosphoproteomics following inducible ribozyme knockdown of PfNIF4 in P. falciparum\",\n      \"pmids\": [\"35938722\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct enzymatic assay or mutagenesis of BDP5 phosphosites was performed\",\n        \"Functional consequence of BDP5 phosphorylation is unknown\",\n        \"Whether PfNIF4 acts directly on BDP5 versus indirectly is not established\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Where BDP5 acts on the genome across the cell cycle was probed by proximity-based chromatin profiling, indicating stage-specific association with open/active chromatin regions.\",\n      \"evidence\": \"DiBioCUT&Tag on FKBP-tagged BDP5 with rapalog-inducible FRB-TurboID at trophozoite and schizont stages in P. falciparum\",\n      \"pmids\": [\"40675147\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"BDP5-specific signal was confounded by free-floating miniTurbo background, making it uninterpretable per the authors\",\n        \"No validated target genes or loci identified\",\n        \"No link between chromatin binding and transcriptional output\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The specific molecular function of BDP5 within the TAF complex, the histone marks its bromodomain reads, and the functional consequences of its PfNIF4-regulated phosphorylation remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No demonstrated bromodomain ligand or histone-mark specificity for BDP5\",\n        \"No loss-of-function phenotype attributing a biological role to BDP5\",\n        \"No causal link between phosphorylation state and chromatin binding or complex function\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0000785\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [\"TAF (TBP-associated-factor) epigenetic reader complex [#0]\"],\n    \"partners\": [\"PfNIF4 phosphatase (regulates BDP5 phosphorylation) [#1]\"],\n    \"other_free_text\": [\n      \"Phosphorylated at T2289, S2291, S2395, T2397 in schizonts; phosphosites accumulate upon PfNIF4 knockdown [#1]\",\n      \"Stage-specific chromatin association reported by DiBioCUT&Tag, but confounded by assay background [#2]\",\n      \"Bromodomain-containing protein; no ligand/histone-mark specificity established in the corpus\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1234100","name":null,"product":"bromodomain protein 5","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1448700","name":null,"product":"bromodomain protein 5, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1453500","name":null,"product":"bromodomain protein 5, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"BDP5","evaluation":null}