{"gene":"TG_257790","gene_symbol":"KDAC4","run_date":"2026-09-08T12:58:25","timeline":{"discoveries":[{"year":2023,"finding":"TgKDAC4 is localized to the apicoplast of Toxoplasma gondii, making it the only lysine deacetylase found in this organelle to date; transmission electron microscopy confirmed its presence at the periphery of the apicoplast.","method":"Transmission electron microscopy (TEM) and subcellular localization assays","journal":"Microorganisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by TEM with functional organelle context, single lab with two orthogonal approaches (imaging + fractionation/IP)","pmids":["37375060"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"finding":"TgKDAC4 is a class IV lysine deacetylase with a KDAC domain of putative prokaryotic origin based on phylogenetic analysis; it shares only a portion of the canonical KDAC domain with other organisms and is unique to apicomplexan parasites.","method":"Phylogenetic analysis of the KDAC domain","journal":"Microorganisms","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational/phylogenetic prediction only, no in vitro enzymatic validation reported in the abstract","pmids":["37375060"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"finding":"Immunoprecipitation followed by mass spectrometry identified TgCPN60 and TgGAPDH2 as putative binding partners or substrates of TgKDAC4; both proteins are located at the apicoplast and contain acetylation sites.","method":"Co-immunoprecipitation followed by mass spectrometry","journal":"Microorganisms","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/MS experiment, single lab, no reciprocal pull-down or functional validation of the interaction reported in the abstract","pmids":["37375060"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"TgKDAC4 is a class IV lysine deacetylase unique to apicomplexan parasites that localizes to the periphery of the Toxoplasma gondii apicoplast, where it putatively deacetylates apicoplast-resident proteins including TgCPN60 and TgGAPDH2, suggesting a role in regulating apicoplast metabolism through post-translational acetylation control."},"narrative":{"mechanistic_narrative":"TgKDAC4 is a class IV lysine deacetylase of Toxoplasma gondii that localizes to the periphery of the apicoplast, where it is the only lysine deacetylase identified in this organelle to date [PMID:37375060]. Beyond this localization, mechanistic characterization is limited: phylogenetic analysis and immunoprecipitation-mass spectrometry point to a KDAC domain of putative prokaryotic origin and to apicoplast-resident candidate substrates TgCPN60 and TgGAPDH2, but these remain uncharacterized biochemically in the available corpus [PMID:37375060]. No enzymatic activity, catalytic mechanism, or functional consequence of deacetylation has been experimentally established.","teleology":[{"year":2023,"claim":"Establishing where a candidate deacetylase acts defined TgKDAC4 as the first lysine deacetylase associated with the Toxoplasma apicoplast, implicating acetylation control in this metabolic organelle.","evidence":"Transmission electron microscopy and subcellular localization/fractionation assays in Toxoplasma gondii","pmids":["37375060"],"confidence":"Medium","gaps":["Localization does not demonstrate deacetylase enzymatic activity","Whether TgKDAC4 sits inside the apicoplast lumen or is peripherally attached is not resolved","Functional role of the enzyme in apicoplast biology is untested"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"claim":"Phylogenetic classification addressed the evolutionary origin of the enzyme, assigning it to class IV with a KDAC domain of putative prokaryotic origin unique to apicomplexans.","evidence":"Phylogenetic analysis of the KDAC domain (computational)","pmids":["37375060"],"confidence":"Low","gaps":["Computational prediction only, no in vitro enzymatic validation","Only a portion of the canonical KDAC domain is shared, leaving catalytic competence unconfirmed","No structural model of the domain"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"claim":"Interaction proteomics began to define candidate substrates, nominating apicoplast-resident acetylated proteins TgCPN60 and TgGAPDH2 as putative partners or substrates.","evidence":"Co-immunoprecipitation followed by mass spectrometry in Toxoplasma gondii","pmids":["37375060"],"confidence":"Low","gaps":["Single Co-IP/MS experiment without reciprocal pull-down or functional validation","Direct deacetylation of these substrates by TgKDAC4 not demonstrated","Cannot distinguish stable interactors from transient enzyme-substrate contacts"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"Whether TgKDAC4 has catalytic deacetylase activity, which apicoplast substrates it deacetylates, and how this regulates apicoplast metabolism remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No in vitro or in vivo demonstration of deacetylase activity","No genetic loss-of-function phenotype reported","Candidate substrate deacetylation not biochemically confirmed"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["TGCPN60","TGGAPDH2"],"other_free_text":["Class IV lysine deacetylase with a KDAC domain of putative prokaryotic origin, unique to apicomplexan parasites [#1]","Localizes to the periphery of the apicoplast; only lysine deacetylase identified in this organelle to date [#0]","Candidate substrates/partners TgCPN60 and TgGAPDH2 are apicoplast-resident acetylated proteins identified by IP-MS [#2]","Enzymatic activity and functional role remain experimentally unvalidated in the available corpus"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"37375060","id":"PMC_37375060","title":"TgKDAC4: A Unique Deacetylase of Toxoplasma's Apicoplast.","date":"2023","source":"Microorganisms","url":"https://pubmed.ncbi.nlm.nih.gov/37375060","citation_count":3,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2936,"output_tokens":766,"usd":0.010149,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5535,"output_tokens":1781,"usd":0.0361,"stage2_stop_reason":"end_turn"},"total_usd":0.046249,"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\": 2023,\n      \"finding\": \"TgKDAC4 is localized to the apicoplast of Toxoplasma gondii, making it the only lysine deacetylase found in this organelle to date; transmission electron microscopy confirmed its presence at the periphery of the apicoplast.\",\n      \"method\": \"Transmission electron microscopy (TEM) and subcellular localization assays\",\n      \"journal\": \"Microorganisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by TEM with functional organelle context, single lab with two orthogonal approaches (imaging + fractionation/IP)\",\n      \"pmids\": [\"37375060\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TgKDAC4 is a class IV lysine deacetylase with a KDAC domain of putative prokaryotic origin based on phylogenetic analysis; it shares only a portion of the canonical KDAC domain with other organisms and is unique to apicomplexan parasites.\",\n      \"method\": \"Phylogenetic analysis of the KDAC domain\",\n      \"journal\": \"Microorganisms\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational/phylogenetic prediction only, no in vitro enzymatic validation reported in the abstract\",\n      \"pmids\": [\"37375060\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Immunoprecipitation followed by mass spectrometry identified TgCPN60 and TgGAPDH2 as putative binding partners or substrates of TgKDAC4; both proteins are located at the apicoplast and contain acetylation sites.\",\n      \"method\": \"Co-immunoprecipitation followed by mass spectrometry\",\n      \"journal\": \"Microorganisms\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/MS experiment, single lab, no reciprocal pull-down or functional validation of the interaction reported in the abstract\",\n      \"pmids\": [\"37375060\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"TgKDAC4 is a class IV lysine deacetylase unique to apicomplexan parasites that localizes to the periphery of the Toxoplasma gondii apicoplast, where it putatively deacetylates apicoplast-resident proteins including TgCPN60 and TgGAPDH2, suggesting a role in regulating apicoplast metabolism through post-translational acetylation control.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TgKDAC4 is a class IV lysine deacetylase of Toxoplasma gondii that localizes to the periphery of the apicoplast, where it is the only lysine deacetylase identified in this organelle to date [#0]. Beyond this localization, mechanistic characterization is limited: phylogenetic analysis and immunoprecipitation-mass spectrometry point to a KDAC domain of putative prokaryotic origin and to apicoplast-resident candidate substrates TgCPN60 and TgGAPDH2, but these remain uncharacterized biochemically in the available corpus [#1, #2]. No enzymatic activity, catalytic mechanism, or functional consequence of deacetylation has been experimentally established.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Establishing where a candidate deacetylase acts defined TgKDAC4 as the first lysine deacetylase associated with the Toxoplasma apicoplast, implicating acetylation control in this metabolic organelle.\",\n      \"evidence\": \"Transmission electron microscopy and subcellular localization/fractionation assays in Toxoplasma gondii\",\n      \"pmids\": [\"37375060\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Localization does not demonstrate deacetylase enzymatic activity\",\n        \"Whether TgKDAC4 sits inside the apicoplast lumen or is peripherally attached is not resolved\",\n        \"Functional role of the enzyme in apicoplast biology is untested\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Phylogenetic classification addressed the evolutionary origin of the enzyme, assigning it to class IV with a KDAC domain of putative prokaryotic origin unique to apicomplexans.\",\n      \"evidence\": \"Phylogenetic analysis of the KDAC domain (computational)\",\n      \"pmids\": [\"37375060\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Computational prediction only, no in vitro enzymatic validation\",\n        \"Only a portion of the canonical KDAC domain is shared, leaving catalytic competence unconfirmed\",\n        \"No structural model of the domain\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Interaction proteomics began to define candidate substrates, nominating apicoplast-resident acetylated proteins TgCPN60 and TgGAPDH2 as putative partners or substrates.\",\n      \"evidence\": \"Co-immunoprecipitation followed by mass spectrometry in Toxoplasma gondii\",\n      \"pmids\": [\"37375060\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single Co-IP/MS experiment without reciprocal pull-down or functional validation\",\n        \"Direct deacetylation of these substrates by TgKDAC4 not demonstrated\",\n        \"Cannot distinguish stable interactors from transient enzyme-substrate contacts\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether TgKDAC4 has catalytic deacetylase activity, which apicoplast substrates it deacetylates, and how this regulates apicoplast metabolism remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No in vitro or in vivo demonstration of deacetylase activity\",\n        \"No genetic loss-of-function phenotype reported\",\n        \"Candidate substrate deacetylation not biochemically confirmed\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004407\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0009507\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [\"TgCPN60\", \"TgGAPDH2\"],\n    \"other_free_text\": [\n      \"Class IV lysine deacetylase with a KDAC domain of putative prokaryotic origin, unique to apicomplexan parasites [#1]\",\n      \"Localizes to the periphery of the apicoplast; only lysine deacetylase identified in this organelle to date [#0]\",\n      \"Candidate substrates/partners TgCPN60 and TgGAPDH2 are apicoplast-resident acetylated proteins identified by IP-MS [#2]\",\n      \"Enzymatic activity and functional role remain experimentally unvalidated in the available corpus\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_257790","name":"KDAC4","product":"lysine deacetylase KDAC4","uniprot_acc":"S8GBW3","chromosome":"TGME49_chrVIIb","start_pos":3814329},{"strain":"GT1","gene_id":"TGGT1_257790","name":null,"product":"histone deacetylase HDAC4","uniprot_acc":null,"chromosome":"TGGT1_chrVIIb","start_pos":3747596},{"strain":"RH88","gene_id":"TGRH88_072110","name":null,"product":"histone deacetylase HDAC4","uniprot_acc":null,"chromosome":"CM023089","start_pos":3849193},{"strain":"VEG","gene_id":"TGVEG_257790","name":null,"product":"histone deacetylase HDAC4","uniprot_acc":"A0A125YJU6","chromosome":"TGVEG_chrVIIb","start_pos":3832691}]}