{"gene":"TG_269190","gene_symbol":"GAPDH2","run_date":"2026-09-08T14:08:29","timeline":{"discoveries":[{"year":2022,"finding":"GAPDH2 (phosphoglyceraldehyde dehydrogenase 2) localizes to the apicoplast of Toxoplasma gondii, as determined by endogenous tagging.","method":"Endogenous tagging / fluorescence localization","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Moderate — direct endogenous tagging in T. gondii with functional follow-up, single lab but multiple orthogonal methods (localization + conditional depletion + metabolic assays)","pmids":["36449552"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"Conditional knockdown of GAPDH2 is critical for tachyzoite proliferation; its depletion inhibits parasite growth, demonstrating an essential role in the lytic cycle.","method":"Conditional depletion (knockdown) with growth arrest phenotype readout","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Moderate — conditional depletion with defined growth phenotype, single lab, multiple metabolic readouts supporting mechanistic conclusion","pmids":["36449552"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"GAPDH2 supplies NADPH (reducing power) to apicoplast metabolic pathways; its knockdown reduces isoprenoid precursor synthesis via the MEP pathway and reduces de novo fatty acid synthesis in the apicoplast.","method":"Conditional depletion combined with measurement of MEP pathway intermediates and fatty acid synthesis assays","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Moderate — conditional depletion with multiple orthogonal metabolic readouts (MEP intermediates and fatty acid synthesis), single lab","pmids":["36449552"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"finding":"TgGAPDH2 was identified as a potential interaction partner or substrate of the apicoplast deacetylase TgKDAC4 by immunoprecipitation followed by mass spectrometry; TgGAPDH2 contains acetylation sites.","method":"Immunoprecipitation followed by mass spectrometry (IP-MS)","journal":"Microorganisms","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/MS identification with no functional validation of the interaction or acetylation in this study","pmids":["37375060"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"GAPDH2 is an apicoplast-localized glycolytic enzyme in Toxoplasma gondii that produces NADPH to supply reducing power for the MEP isoprenoid precursor synthesis pathway, de novo fatty acid synthesis, and the ferredoxin redox system within the apicoplast, and is essential for tachyzoite proliferation; it may also be subject to acetylation-based regulation by the apicoplast deacetylase TgKDAC4."},"narrative":{"mechanistic_narrative":"GAPDH2 is an apicoplast-localized enzyme of Toxoplasma gondii that supplies reducing power to organellar metabolism and is required for tachyzoite proliferation [PMID:36449552]. Endogenous tagging places the protein within the apicoplast [PMID:36449552], and conditional depletion arrests parasite growth in the lytic cycle [PMID:36449552]. Functionally, GAPDH2 provides NADPH to apicoplast pathways: its loss reduces isoprenoid precursor synthesis through the MEP pathway and diminishes de novo fatty acid synthesis in the organelle [PMID:36449552]. Beyond this metabolic role, no further mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2022,"claim":"Establishing where GAPDH2 acts was the first step; endogenous tagging localized it to the apicoplast, distinguishing it from cytosolic glycolytic enzymes and framing a role in organellar metabolism.","evidence":"Endogenous tagging and fluorescence localization in T. gondii","pmids":["36449552"],"confidence":"High","gaps":["Sub-organellar localization within the apicoplast not resolved","Import/targeting mechanism not defined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"Whether GAPDH2 is dispensable was tested by conditional knockdown, which arrested tachyzoite growth and established the enzyme as essential to the lytic cycle.","evidence":"Conditional depletion with growth-arrest phenotype readout in T. gondii","pmids":["36449552"],"confidence":"High","gaps":["Whether growth arrest reflects a single metabolic deficit or pleiotropic effects not dissected","Requirement in other life-cycle stages (bradyzoite, in vivo) not addressed"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"The metabolic consequence of depletion was measured to define GAPDH2's biochemical output, showing it supplies NADPH that feeds the MEP isoprenoid pathway and de novo fatty acid synthesis in the apicoplast.","evidence":"Conditional depletion combined with quantification of MEP pathway intermediates and fatty acid synthesis assays in T. gondii","pmids":["36449552"],"confidence":"High","gaps":["Direct enzymatic characterization (NADPH-dependent kinetics) not reported","Contribution to the ferredoxin redox system not directly measured","Whether NADPH supply is the sole essential function unresolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"claim":"Whether GAPDH2 activity is post-translationally regulated was probed by identifying it as a candidate interactor/substrate of the apicoplast deacetylase TgKDAC4, raising the possibility of acetylation-based control.","evidence":"Immunoprecipitation followed by mass spectrometry identifying TgGAPDH2 with acetylation sites in T. gondii","pmids":["37375060"],"confidence":"Low","gaps":["Single Co-IP/MS identification with no functional validation of the interaction or acetylation","Effect of acetylation on GAPDH2 enzymatic activity not tested","No reciprocal validation of the TgKDAC4 interaction"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"How GAPDH2 is enzymatically regulated and whether its acetylation state modulates apicoplast NADPH supply remain open.","evidence":"","pmids":[],"confidence":"Low","gaps":["No functional link established between TgKDAC4-mediated deacetylation and GAPDH2 activity","No structural or kinetic model of the enzyme","Role across life-cycle stages and in vivo not characterized"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["TGKDAC4 (CANDIDATE INTERACTOR/DEACETYLASE, IP-MS ONLY) [#3]"],"other_free_text":["Essential for tachyzoite proliferation in the lytic cycle [#1]","Contains acetylation sites identified by IP-MS [#3]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"36449552","id":"PMC_36449552","title":"Two apicoplast dwelling glycolytic enzymes provide key substrates for metabolic pathways in the apicoplast and are critical for Toxoplasma growth.","date":"2022","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/36449552","citation_count":20,"is_preprint":false},{"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":3617,"output_tokens":967,"usd":0.012678,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5871,"output_tokens":2087,"usd":0.040765,"stage2_stop_reason":"end_turn"},"total_usd":0.053443,"stage1_batch_id":"msgbatch_015xmQKDRqnTh9anE4m7LiD6","stage2_batch_id":"msgbatch_01JLpkFTVhoQBNgqHCKFrVVU","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2022,\n      \"finding\": \"GAPDH2 (phosphoglyceraldehyde dehydrogenase 2) localizes to the apicoplast of Toxoplasma gondii, as determined by endogenous tagging.\",\n      \"method\": \"Endogenous tagging / fluorescence localization\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct endogenous tagging in T. gondii with functional follow-up, single lab but multiple orthogonal methods (localization + conditional depletion + metabolic assays)\",\n      \"pmids\": [\"36449552\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Conditional knockdown of GAPDH2 is critical for tachyzoite proliferation; its depletion inhibits parasite growth, demonstrating an essential role in the lytic cycle.\",\n      \"method\": \"Conditional depletion (knockdown) with growth arrest phenotype readout\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional depletion with defined growth phenotype, single lab, multiple metabolic readouts supporting mechanistic conclusion\",\n      \"pmids\": [\"36449552\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"GAPDH2 supplies NADPH (reducing power) to apicoplast metabolic pathways; its knockdown reduces isoprenoid precursor synthesis via the MEP pathway and reduces de novo fatty acid synthesis in the apicoplast.\",\n      \"method\": \"Conditional depletion combined with measurement of MEP pathway intermediates and fatty acid synthesis assays\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional depletion with multiple orthogonal metabolic readouts (MEP intermediates and fatty acid synthesis), single lab\",\n      \"pmids\": [\"36449552\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TgGAPDH2 was identified as a potential interaction partner or substrate of the apicoplast deacetylase TgKDAC4 by immunoprecipitation followed by mass spectrometry; TgGAPDH2 contains acetylation sites.\",\n      \"method\": \"Immunoprecipitation followed by mass spectrometry (IP-MS)\",\n      \"journal\": \"Microorganisms\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/MS identification with no functional validation of the interaction or acetylation in this study\",\n      \"pmids\": [\"37375060\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"GAPDH2 is an apicoplast-localized glycolytic enzyme in Toxoplasma gondii that produces NADPH to supply reducing power for the MEP isoprenoid precursor synthesis pathway, de novo fatty acid synthesis, and the ferredoxin redox system within the apicoplast, and is essential for tachyzoite proliferation; it may also be subject to acetylation-based regulation by the apicoplast deacetylase TgKDAC4.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"GAPDH2 is an apicoplast-localized enzyme of Toxoplasma gondii that supplies reducing power to organellar metabolism and is required for tachyzoite proliferation [#0, #1]. Endogenous tagging places the protein within the apicoplast [#0], and conditional depletion arrests parasite growth in the lytic cycle [#1]. Functionally, GAPDH2 provides NADPH to apicoplast pathways: its loss reduces isoprenoid precursor synthesis through the MEP pathway and diminishes de novo fatty acid synthesis in the organelle [#2]. Beyond this metabolic role, no further mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Establishing where GAPDH2 acts was the first step; endogenous tagging localized it to the apicoplast, distinguishing it from cytosolic glycolytic enzymes and framing a role in organellar metabolism.\",\n      \"evidence\": \"Endogenous tagging and fluorescence localization in T. gondii\",\n      \"pmids\": [\"36449552\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Sub-organellar localization within the apicoplast not resolved\",\n        \"Import/targeting mechanism not defined\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Whether GAPDH2 is dispensable was tested by conditional knockdown, which arrested tachyzoite growth and established the enzyme as essential to the lytic cycle.\",\n      \"evidence\": \"Conditional depletion with growth-arrest phenotype readout in T. gondii\",\n      \"pmids\": [\"36449552\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether growth arrest reflects a single metabolic deficit or pleiotropic effects not dissected\",\n        \"Requirement in other life-cycle stages (bradyzoite, in vivo) not addressed\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"The metabolic consequence of depletion was measured to define GAPDH2's biochemical output, showing it supplies NADPH that feeds the MEP isoprenoid pathway and de novo fatty acid synthesis in the apicoplast.\",\n      \"evidence\": \"Conditional depletion combined with quantification of MEP pathway intermediates and fatty acid synthesis assays in T. gondii\",\n      \"pmids\": [\"36449552\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct enzymatic characterization (NADPH-dependent kinetics) not reported\",\n        \"Contribution to the ferredoxin redox system not directly measured\",\n        \"Whether NADPH supply is the sole essential function unresolved\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether GAPDH2 activity is post-translationally regulated was probed by identifying it as a candidate interactor/substrate of the apicoplast deacetylase TgKDAC4, raising the possibility of acetylation-based control.\",\n      \"evidence\": \"Immunoprecipitation followed by mass spectrometry identifying TgGAPDH2 with acetylation sites in T. gondii\",\n      \"pmids\": [\"37375060\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single Co-IP/MS identification with no functional validation of the interaction or acetylation\",\n        \"Effect of acetylation on GAPDH2 enzymatic activity not tested\",\n        \"No reciprocal validation of the TgKDAC4 interaction\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How GAPDH2 is enzymatically regulated and whether its acetylation state modulates apicoplast NADPH supply remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No functional link established between TgKDAC4-mediated deacetylation and GAPDH2 activity\",\n        \"No structural or kinetic model of the enzyme\",\n        \"Role across life-cycle stages and in vivo not characterized\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004616\", \"supporting_discovery_ids\": [2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0050661\", \"supporting_discovery_ids\": [2], \"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      {\"term_id\": \"GO:0019288\", \"supporting_discovery_ids\": [2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0006633\", \"supporting_discovery_ids\": [2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"TgKDAC4 (candidate interactor/deacetylase, IP-MS only) [#3]\"\n    ],\n    \"other_free_text\": [\n      \"Essential for tachyzoite proliferation in the lytic cycle [#1]\",\n      \"Contains acetylation sites identified by IP-MS [#3]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_269190","name":"GAPDH2","product":"glyceraldehyde-3-phosphate dehydrogenase GAPDH2","uniprot_acc":"A0A125YM60","chromosome":"TGME49_chrVIII","start_pos":6002854},{"strain":"GT1","gene_id":"TGGT1_269190","name":null,"product":"glyceraldehyde-3-phosphate dehydrogenase GAPDH2","uniprot_acc":null,"chromosome":"TGGT1_chrVIII","start_pos":6001367},{"strain":"RH88","gene_id":"TGRH88_082060","name":null,"product":"glyceraldehyde-3-phosphate dehydrogenase GAPDH2","uniprot_acc":null,"chromosome":"CM023089","start_pos":11121421},{"strain":"VEG","gene_id":"TGVEG_269190","name":null,"product":"glyceraldehyde-3-phosphate dehydrogenase GAPDH2","uniprot_acc":"V5BMS8","chromosome":"TGVEG_chrVIII","start_pos":6018561}]}