{"gene":"PF3D7_1212900","run_date":"2026-09-08T14:19:06","timeline":{"discoveries":[{"year":2012,"finding":"PF3D7_1212900 (BDP2) was identified as a nuclear protein in P. falciparum by organellar proteomics combined with experimental validation using transgenic cell lines, establishing its nuclear localization.","method":"High-accuracy mass spectrometry of nuclear proteome fractions; experimental validation with transgenic cell lines (nuclear localization confirmed)","journal":"Genome biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — nuclear fractionation coupled with MS and transgenic validation, single lab but two orthogonal methods","pmids":["23181666"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"BDP2 (PF3D7_1212900) physically interacts with PfBDP1, as identified by co-immunoprecipitation/interaction proteomics, suggesting BDP2 participates in a bromodomain protein complex involved in invasion gene regulation.","method":"Co-immunoprecipitation / interaction proteomics (BDP1 pulldown identifying BDP2 as binding partner)","journal":"Cell host & microbe","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP/pulldown identifying BDP2 as a BDP1-interacting partner; reported in this paper and corroborated in subsequent studies","pmids":["26067602"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2019,"finding":"BDP2 (PF3D7_1212900) is a component of the BDP1/BDP2 complex that is recruited to chromatin in an acetylation-level-dependent manner, as revealed by histone peptide pull-downs with acetylated histone marks and quantitative interaction proteomics.","method":"Histone peptide pull-downs with acetylated PTMs followed by quantitative proteomics; tagging and interaction proteomics","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — histone peptide pull-down plus quantitative interaction proteomics in a single lab with two orthogonal approaches","pmids":["31728527"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"finding":"BDP2 (PF3D7_1212900) is a constitutive component of the BDP1/BDP2 core complex; this complex also includes PfBDP7, and together BDP1 and BDP7 (not BDP2 directly tested in this study) associate with heterochromatic regions across variant surface antigen (VSA) gene bodies to contribute to their silencing.","method":"Interaction proteomics confirming BDP2 in the BDP1/BDP2/BDP7 complex; ChIP-seq and conditional knockdown of BDP1 and BDP7","journal":"Frontiers in cell and developmental biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — BDP2's role in the complex is inferred from its membership; direct functional experiments were performed on BDP1 and BDP7, not BDP2 itself","pmids":["35493110"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"BDP2 (PF3D7_1212900) is a nuclear bromodomain protein in P. falciparum that physically interacts with PfBDP1 to form a core BDP1/BDP2 complex; this complex is recruited to chromatin in an acetylation-level-dependent manner and is implicated in the regulation of invasion-related genes, though direct functional experiments (knockdown/knockout with phenotypic readouts) have been performed on PfBDP1 rather than on BDP2 itself."},"narrative":{"mechanistic_narrative":"BDP2 (PF3D7_1212900) is a nuclear bromodomain protein of Plasmodium falciparum that functions as a constitutive partner of PfBDP1 within a chromatin-associated bromodomain protein complex [PMID:23181666, PMID:26067602, PMID:35493110]. It was first placed in the nucleus by organellar proteomics with transgenic validation [PMID:23181666], and subsequently shown to physically associate with PfBDP1 in interaction proteomics, defining a core BDP1/BDP2 module [PMID:26067602]. This complex is recruited to chromatin in an acetylation-level-dependent manner, as demonstrated by acetylated histone peptide pull-downs coupled to quantitative interaction proteomics, linking BDP2 to acetylation-marked chromatin and the regulation of invasion-related genes [PMID:26067602, PMID:31728527]. BDP2 is also a member of a larger BDP1/BDP2/BDP7 assembly associated with variant surface antigen gene silencing, but the direct functional experiments (conditional knockdown, ChIP-seq) in that context were performed on PfBDP1 and PfBDP7 rather than on BDP2 itself [PMID:35493110]. Beyond its membership in these complexes and its acetylation-dependent chromatin recruitment, no BDP2-specific loss-of-function phenotype has been characterized in the available corpus.","teleology":[{"year":2012,"claim":"Establishing where BDP2 acts was the first question; localizing it to the nucleus positioned it as a candidate chromatin-associated factor rather than a cytoplasmic protein.","evidence":"High-accuracy mass spectrometry of nuclear proteome fractions with transgenic cell line validation in P. falciparum","pmids":["23181666"],"confidence":"Medium","gaps":["Localization alone does not define a molecular activity or binding partners","No chromatin-binding specificity established at this stage"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Whether BDP2 works alone or within a complex was resolved by showing it physically associates with PfBDP1, placing BDP2 in a bromodomain protein complex tied to invasion gene regulation.","evidence":"Co-immunoprecipitation / interaction proteomics via BDP1 pulldown identifying BDP2 in P. falciparum","pmids":["26067602"],"confidence":"Medium","gaps":["Single Co-IP without reciprocal BDP2 pulldown reported","Direct contribution of BDP2 to invasion gene regulation not tested","Stoichiometry and interaction interface unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2019,"claim":"How the BDP1/BDP2 complex finds chromatin was addressed by demonstrating acetylation-level-dependent recruitment, connecting BDP2 to acetylated histone marks.","evidence":"Acetylated histone peptide pull-downs plus quantitative interaction proteomics and tagging in P. falciparum","pmids":["31728527"],"confidence":"Medium","gaps":["Which specific acetyl marks BDP2's own bromodomain reads was not resolved separately from BDP1","Direct DNA/chromatin binding by BDP2 not distinguished from complex-level recruitment"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"claim":"The composition of the complex was extended to include PfBDP7 and linked to variant surface antigen silencing, but BDP2's specific role remained inferred from membership rather than tested directly.","evidence":"Interaction proteomics confirming BDP2 in the BDP1/BDP2/BDP7 complex, with ChIP-seq and conditional knockdown performed on BDP1 and BDP7 in P. falciparum","pmids":["35493110"],"confidence":"Low","gaps":["No conditional knockdown or knockout of BDP2 itself performed; its function is inferred from complex membership","Whether BDP2 is required for VSA silencing is untested","BDP2's contribution distinct from BDP1/BDP7 is undefined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The direct functional role of BDP2 remains unresolved: no BDP2-specific loss-of-function phenotype, target gene set, or bromodomain acetyl-mark specificity has been established independent of its complex partners.","evidence":"No discovery in the corpus performs BDP2-specific perturbation with phenotypic readout","pmids":[],"confidence":"Low","gaps":["BDP2 knockdown/knockout phenotype unknown","BDP2 bromodomain ligand specificity uncharacterized","Contribution of BDP2 to invasion gene versus VSA gene regulation undetermined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["BDP1/BDP2 core complex","BDP1/BDP2/BDP7 complex"],"partners":["PFBDP1","PFBDP7"],"other_free_text":["BDP2 (PF3D7_1212900) is established chiefly as a constitutive member of the PfBDP1-containing bromodomain complex; direct functional experiments in the corpus were performed on PfBDP1 and PfBDP7, not on BDP2 itself.","Complex recruitment to chromatin is acetylation-level-dependent, connecting BDP2 to acetylated histone marks and to regulation of invasion-related and variant surface antigen genes."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"23181666","id":"PMC_23181666","title":"Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum.","date":"2012","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/23181666","citation_count":120,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26067602","id":"PMC_26067602","title":"A Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression.","date":"2015","source":"Cell host & microbe","url":"https://pubmed.ncbi.nlm.nih.gov/26067602","citation_count":90,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfBDP2"],"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":["BDP2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35493110","id":"PMC_35493110","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":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["BDP2","PfBDP2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4923,"output_tokens":1115,"usd":0.015747,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5955,"output_tokens":2540,"usd":0.046637,"stage2_stop_reason":"end_turn"},"total_usd":0.062384,"stage1_batch_id":"msgbatch_011BPjN2BL33F8cJXD1r7V7T","stage2_batch_id":"msgbatch_01Qwg6vP7qxkpL6Gsc7tajsb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"PF3D7_1212900 (BDP2) was identified as a nuclear protein in P. falciparum by organellar proteomics combined with experimental validation using transgenic cell lines, establishing its nuclear localization.\",\n      \"method\": \"High-accuracy mass spectrometry of nuclear proteome fractions; experimental validation with transgenic cell lines (nuclear localization confirmed)\",\n      \"journal\": \"Genome biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — nuclear fractionation coupled with MS and transgenic validation, single lab but two orthogonal methods\",\n      \"pmids\": [\"23181666\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"BDP2 (PF3D7_1212900) physically interacts with PfBDP1, as identified by co-immunoprecipitation/interaction proteomics, suggesting BDP2 participates in a bromodomain protein complex involved in invasion gene regulation.\",\n      \"method\": \"Co-immunoprecipitation / interaction proteomics (BDP1 pulldown identifying BDP2 as binding partner)\",\n      \"journal\": \"Cell host & microbe\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP/pulldown identifying BDP2 as a BDP1-interacting partner; reported in this paper and corroborated in subsequent studies\",\n      \"pmids\": [\"26067602\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"BDP2 (PF3D7_1212900) is a component of the BDP1/BDP2 complex that is recruited to chromatin in an acetylation-level-dependent manner, as revealed by histone peptide pull-downs with acetylated histone marks and quantitative interaction proteomics.\",\n      \"method\": \"Histone peptide pull-downs with acetylated PTMs followed by quantitative proteomics; tagging and interaction proteomics\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — histone peptide pull-down plus quantitative interaction proteomics in a single lab with two orthogonal approaches\",\n      \"pmids\": [\"31728527\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"BDP2 (PF3D7_1212900) is a constitutive component of the BDP1/BDP2 core complex; this complex also includes PfBDP7, and together BDP1 and BDP7 (not BDP2 directly tested in this study) associate with heterochromatic regions across variant surface antigen (VSA) gene bodies to contribute to their silencing.\",\n      \"method\": \"Interaction proteomics confirming BDP2 in the BDP1/BDP2/BDP7 complex; ChIP-seq and conditional knockdown of BDP1 and BDP7\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — BDP2's role in the complex is inferred from its membership; direct functional experiments were performed on BDP1 and BDP7, not BDP2 itself\",\n      \"pmids\": [\"35493110\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"BDP2 (PF3D7_1212900) is a nuclear bromodomain protein in P. falciparum that physically interacts with PfBDP1 to form a core BDP1/BDP2 complex; this complex is recruited to chromatin in an acetylation-level-dependent manner and is implicated in the regulation of invasion-related genes, though direct functional experiments (knockdown/knockout with phenotypic readouts) have been performed on PfBDP1 rather than on BDP2 itself.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"BDP2 (PF3D7_1212900) is a nuclear bromodomain protein of Plasmodium falciparum that functions as a constitutive partner of PfBDP1 within a chromatin-associated bromodomain protein complex [#0, #1, #3]. It was first placed in the nucleus by organellar proteomics with transgenic validation [#0], and subsequently shown to physically associate with PfBDP1 in interaction proteomics, defining a core BDP1/BDP2 module [#1]. This complex is recruited to chromatin in an acetylation-level-dependent manner, as demonstrated by acetylated histone peptide pull-downs coupled to quantitative interaction proteomics, linking BDP2 to acetylation-marked chromatin and the regulation of invasion-related genes [#1, #2]. BDP2 is also a member of a larger BDP1/BDP2/BDP7 assembly associated with variant surface antigen gene silencing, but the direct functional experiments (conditional knockdown, ChIP-seq) in that context were performed on PfBDP1 and PfBDP7 rather than on BDP2 itself [#3]. Beyond its membership in these complexes and its acetylation-dependent chromatin recruitment, no BDP2-specific loss-of-function phenotype has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Establishing where BDP2 acts was the first question; localizing it to the nucleus positioned it as a candidate chromatin-associated factor rather than a cytoplasmic protein.\",\n      \"evidence\": \"High-accuracy mass spectrometry of nuclear proteome fractions with transgenic cell line validation in P. falciparum\",\n      \"pmids\": [\n        \"23181666\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Localization alone does not define a molecular activity or binding partners\",\n        \"No chromatin-binding specificity established at this stage\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Whether BDP2 works alone or within a complex was resolved by showing it physically associates with PfBDP1, placing BDP2 in a bromodomain protein complex tied to invasion gene regulation.\",\n      \"evidence\": \"Co-immunoprecipitation / interaction proteomics via BDP1 pulldown identifying BDP2 in P. falciparum\",\n      \"pmids\": [\n        \"26067602\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single Co-IP without reciprocal BDP2 pulldown reported\",\n        \"Direct contribution of BDP2 to invasion gene regulation not tested\",\n        \"Stoichiometry and interaction interface unknown\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"How the BDP1/BDP2 complex finds chromatin was addressed by demonstrating acetylation-level-dependent recruitment, connecting BDP2 to acetylated histone marks.\",\n      \"evidence\": \"Acetylated histone peptide pull-downs plus quantitative interaction proteomics and tagging in P. falciparum\",\n      \"pmids\": [\n        \"31728527\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Which specific acetyl marks BDP2's own bromodomain reads was not resolved separately from BDP1\",\n        \"Direct DNA/chromatin binding by BDP2 not distinguished from complex-level recruitment\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"The composition of the complex was extended to include PfBDP7 and linked to variant surface antigen silencing, but BDP2's specific role remained inferred from membership rather than tested directly.\",\n      \"evidence\": \"Interaction proteomics confirming BDP2 in the BDP1/BDP2/BDP7 complex, with ChIP-seq and conditional knockdown performed on BDP1 and BDP7 in P. falciparum\",\n      \"pmids\": [\n        \"35493110\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No conditional knockdown or knockout of BDP2 itself performed; its function is inferred from complex membership\",\n        \"Whether BDP2 is required for VSA silencing is untested\",\n        \"BDP2's contribution distinct from BDP1/BDP7 is undefined\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct functional role of BDP2 remains unresolved: no BDP2-specific loss-of-function phenotype, target gene set, or bromodomain acetyl-mark specificity has been established independent of its complex partners.\",\n      \"evidence\": \"No discovery in the corpus performs BDP2-specific perturbation with phenotypic readout\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"BDP2 knockdown/knockout phenotype unknown\",\n        \"BDP2 bromodomain ligand specificity uncharacterized\",\n        \"Contribution of BDP2 to invasion gene versus VSA gene regulation undetermined\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0140033\",\n        \"supporting_discovery_ids\": [\n          2\n        ]\n      },\n      {\n        \"term_id\": \"GO:0070577\",\n        \"supporting_discovery_ids\": [\n          2\n        ]\n      }\n    ],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0005634\",\n        \"supporting_discovery_ids\": [\n          0\n        ]\n      },\n      {\n        \"term_id\": \"GO:0000785\",\n        \"supporting_discovery_ids\": [\n          2,\n          3\n        ]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0006325\",\n        \"supporting_discovery_ids\": [\n          2,\n          3\n        ]\n      },\n      {\n        \"term_id\": \"GO:0006342\",\n        \"supporting_discovery_ids\": [\n          3\n        ]\n      }\n    ],\n    \"complexes\": [\n      \"BDP1/BDP2 core complex\",\n      \"BDP1/BDP2/BDP7 complex\"\n    ],\n    \"partners\": [\n      \"PfBDP1\",\n      \"PfBDP7\"\n    ],\n    \"other_free_text\": [\n      \"BDP2 (PF3D7_1212900) is established chiefly as a constitutive member of the PfBDP1-containing bromodomain complex; direct functional experiments in the corpus were performed on PfBDP1 and PfBDP7, not on BDP2 itself.\",\n      \"Complex recruitment to chromatin is acetylation-level-dependent, connecting BDP2 to acetylated histone marks and to regulation of invasion-related and variant surface antigen genes.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1212900","name":null,"product":"bromodomain protein 2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1428900","name":null,"product":"bromodomain protein 2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1432300","name":null,"product":"bromodomain protein 2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"BDP2","evaluation":null}