{"gene":"TG_245670","gene_symbol":"PDHE1A","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2008,"finding":"The pyruvate dehydrogenase complex (PDH), which includes the E1Alpha subunit (PDHE1A), is exclusively localised inside the apicoplast of T. gondii and is absent from the mitochondrion, as determined by expression of epitope-tagged fusion proteins.","method":"Epitope-tagged fusion protein expression and subcellular localization","journal":"International journal for parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with epitope-tagged protein, single lab, single method","pmids":["18336823"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2020,"finding":"CRISPR/Cas9-assisted deletion of the pdh-e1α gene (PDHE1A) in T. gondii tachyzoites produced viable parasites with impaired growth and concurrent loss of the apicoplast, but normal virulence in mice; metabolic labeling of the Δpdh-e1α mutant showed reduced incorporation of glucose-derived carbon into medium-chain fatty acids (C14:0 and C16:0), demonstrating that apicoplast-localized PDH drives de novo fatty acid biosynthesis via FAS2.","method":"CRISPR/Cas9 gene deletion, metabolic labeling, mouse virulence assay, fatty acid supplementation rescue","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO with defined cellular and metabolic phenotype, multiple orthogonal methods (genetic deletion, isotope tracing, rescue by exogenous fatty acids, in vivo virulence), single lab","pmids":["32341123"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2020,"finding":"The apicoplast pyruvate dehydrogenase complex (PDH), which includes PDHE1A, generates the acetyl-CoA pool dedicated to de novo fatty acid synthesis within the apicoplast; multi-omics profiling of parasites lacking other acetyl-CoA-generating enzymes confirmed the distinct, compartment-specific role of the PDH-derived apicoplast acetyl-CoA pool.","method":"Multi-omics (acetylome, transcriptome, proteome, metabolome) of parasite mutants lacking other acetyl-CoA enzymes","journal":"BMC biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multi-omics approach in single lab; PDH role inferred from complementary mutant analysis rather than direct PDH KO in this study","pmids":["32546260"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"PDHE1A is the E1Alpha subunit of the pyruvate dehydrogenase complex (PDH) that localizes exclusively to the apicoplast of T. gondii, where it converts pyruvate to acetyl-CoA to fuel the apicoplast-based type 2 fatty acid synthesis (FAS2) pathway; genetic deletion of PDHE1A impairs growth and causes apicoplast loss but is dispensable in vivo because tachyzoites can salvage host-derived fatty acids."},"narrative":{"mechanistic_narrative":"PDHE1A is the E1Alpha subunit of the pyruvate dehydrogenase complex (PDH) in Toxoplasma gondii, where it functions within an apicoplast-based pathway that converts pyruvate into the acetyl-CoA pool used for de novo fatty acid biosynthesis [PMID:18336823, PMID:32341123]. In contrast to the mitochondrial PDH of most eukaryotes, this complex localizes exclusively to the apicoplast and is absent from the mitochondrion [PMID:18336823]. The apicoplast PDH generates a distinct, compartment-specific acetyl-CoA pool dedicated to the FAS2 pathway [PMID:32546260], and CRISPR/Cas9 deletion of pdh-e1α reduces incorporation of glucose-derived carbon into medium-chain fatty acids (C14:0 and C16:0), producing parasites with impaired growth and loss of the apicoplast while retaining normal virulence in mice owing to salvage of host-derived fatty acids [PMID:32341123]. Nothing further about PDHE1A has been characterized in the available corpus.","teleology":[{"year":2008,"claim":"Establishing where PDH operates in T. gondii was needed because the canonical PDH is mitochondrial; localizing the complex fixed the compartment in which PDHE1A acts.","evidence":"Expression of epitope-tagged fusion proteins and subcellular localization","pmids":["18336823"],"confidence":"Medium","gaps":["Localization based on tagged fusion proteins in a single lab","Does not establish the metabolic function of the compartmentalized complex"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2020,"claim":"Whether apicoplast PDH actually drives fatty acid synthesis and is essential was unresolved; direct deletion showed PDHE1A supplies carbon for de novo fatty acid biosynthesis and is required for apicoplast maintenance but dispensable in vivo via host lipid salvage.","evidence":"CRISPR/Cas9 deletion of pdh-e1α, glucose metabolic labeling, fatty acid supplementation rescue, and mouse virulence assay","pmids":["32341123"],"confidence":"High","gaps":["Mechanism of apicoplast loss upon deletion not resolved","Enzymatic parameters of the PDHE1A subunit not defined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2020,"claim":"It was unclear whether apicoplast PDH provides a functionally distinct acetyl-CoA pool; multi-omics of mutants in other acetyl-CoA enzymes confirmed the PDH-derived pool is compartment-specific and dedicated to fatty acid synthesis.","evidence":"Multi-omics (acetylome, transcriptome, proteome, metabolome) of parasites lacking other acetyl-CoA-generating enzymes","pmids":["32546260"],"confidence":"Medium","gaps":["PDH role inferred from complementary mutants rather than direct PDH KO in this study","Does not resolve regulation of the PDH pool"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Pyruvate dehydrogenase complex (apicoplast PDH)"],"partners":[],"other_free_text":["Deletion of pdh-e1α causes apicoplast loss and impaired growth but preserves mouse virulence via host fatty acid salvage","PDH activity is increased by dichloroacetate, consistent with regulation by PDK kinases"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"25032958","id":"PMC_25032958","title":"BCKDH: the missing link in apicomplexan mitochondrial metabolism is required for full virulence of Toxoplasma gondii and Plasmodium berghei.","date":"2014","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/25032958","citation_count":102,"is_preprint":false},{"pmid":"18336823","id":"PMC_18336823","title":"Localisation of gluconeogenesis and tricarboxylic acid (TCA)-cycle enzymes and first functional analysis of the TCA cycle in Toxoplasma gondii.","date":"2008","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/18336823","citation_count":43,"is_preprint":false},{"pmid":"32341123","id":"PMC_32341123","title":"Acquisition of exogenous fatty acids renders apicoplast-based biosynthesis dispensable in tachyzoites of Toxoplasma.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32341123","citation_count":42,"is_preprint":false},{"pmid":"32546260","id":"PMC_32546260","title":"Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii.","date":"2020","source":"BMC biology","url":"https://pubmed.ncbi.nlm.nih.gov/32546260","citation_count":39,"is_preprint":false},{"pmid":"33408226","id":"PMC_33408226","title":"Dichloroacetate and Pyruvate Metabolism: Pyruvate Dehydrogenase Kinases as Targets Worth Investigating for Effective Therapy of Toxoplasmosis.","date":"2021","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/33408226","citation_count":9,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5339,"output_tokens":1560,"usd":0.019709,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6763,"output_tokens":2820,"usd":0.052158,"stage2_stop_reason":"end_turn"},"total_usd":0.132679,"stage1_batch_id":"msgbatch_01TEPNZ4MCzJ7xtsNwosiDRk","stage2_batch_id":"msgbatch_01FQShM7n1sfCr4pWTDShmki","note":"batch pricing = 50% of standard","corrective_rerun":"2026-09-10 wrong-gene rerun (round-4 rules)","corrective_reason":"re-read with subject anchor"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"The pyruvate dehydrogenase complex (PDH), which includes the E1Alpha subunit (PDHE1A), is exclusively localised inside the apicoplast of T. gondii and is absent from the mitochondrion, as determined by expression of epitope-tagged fusion proteins.\",\n      \"method\": \"Epitope-tagged fusion protein expression and subcellular localization\",\n      \"journal\": \"International journal for parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with epitope-tagged protein, single lab, single method\",\n      \"pmids\": [\"18336823\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CRISPR/Cas9-assisted deletion of the pdh-e1α gene (PDHE1A) in T. gondii tachyzoites produced viable parasites with impaired growth and concurrent loss of the apicoplast, but normal virulence in mice; metabolic labeling of the Δpdh-e1α mutant showed reduced incorporation of glucose-derived carbon into medium-chain fatty acids (C14:0 and C16:0), demonstrating that apicoplast-localized PDH drives de novo fatty acid biosynthesis via FAS2.\",\n      \"method\": \"CRISPR/Cas9 gene deletion, metabolic labeling, mouse virulence assay, fatty acid supplementation rescue\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO with defined cellular and metabolic phenotype, multiple orthogonal methods (genetic deletion, isotope tracing, rescue by exogenous fatty acids, in vivo virulence), single lab\",\n      \"pmids\": [\"32341123\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The apicoplast pyruvate dehydrogenase complex (PDH), which includes PDHE1A, generates the acetyl-CoA pool dedicated to de novo fatty acid synthesis within the apicoplast; multi-omics profiling of parasites lacking other acetyl-CoA-generating enzymes confirmed the distinct, compartment-specific role of the PDH-derived apicoplast acetyl-CoA pool.\",\n      \"method\": \"Multi-omics (acetylome, transcriptome, proteome, metabolome) of parasite mutants lacking other acetyl-CoA enzymes\",\n      \"journal\": \"BMC biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multi-omics approach in single lab; PDH role inferred from complementary mutant analysis rather than direct PDH KO in this study\",\n      \"pmids\": [\"32546260\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Dichloroacetate (DCA) treatment increased pyruvate dehydrogenase (PDH) activity in T. gondii and caused unbalanced mitochondrial activity and morphological alterations in mitochondria and apicoplasts, consistent with PDH being a regulatory target of PDK kinases in the parasite.\",\n      \"method\": \"PDH enzyme activity assay, DCA pharmacological treatment, organelle morphology analysis\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — enzyme activity assay with pharmacological agent, indirect evidence for PDHE1A regulation; single lab, single method, no direct genetic manipulation of PDHE1A\",\n      \"pmids\": [\"33408226\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PDHE1A is the E1Alpha subunit of the pyruvate dehydrogenase complex (PDH) that localizes exclusively to the apicoplast of T. gondii, where it converts pyruvate to acetyl-CoA to fuel the apicoplast-based type 2 fatty acid synthesis (FAS2) pathway; genetic deletion of PDHE1A impairs growth and causes apicoplast loss but is dispensable in vivo because tachyzoites can salvage host-derived fatty acids.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PDHE1A is the E1Alpha subunit of the pyruvate dehydrogenase complex (PDH) in Toxoplasma gondii, where it functions within an apicoplast-based pathway that converts pyruvate into the acetyl-CoA pool used for de novo fatty acid biosynthesis [#0, #1]. In contrast to the mitochondrial PDH of most eukaryotes, this complex localizes exclusively to the apicoplast and is absent from the mitochondrion [#0]. The apicoplast PDH generates a distinct, compartment-specific acetyl-CoA pool dedicated to the FAS2 pathway [#2], and CRISPR/Cas9 deletion of pdh-e1\\u03b1 reduces incorporation of glucose-derived carbon into medium-chain fatty acids (C14:0 and C16:0), producing parasites with impaired growth and loss of the apicoplast while retaining normal virulence in mice owing to salvage of host-derived fatty acids [#1]. Nothing further about PDHE1A has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Establishing where PDH operates in T. gondii was needed because the canonical PDH is mitochondrial; localizing the complex fixed the compartment in which PDHE1A acts.\",\n      \"evidence\": \"Expression of epitope-tagged fusion proteins and subcellular localization\",\n      \"pmids\": [\"18336823\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Localization based on tagged fusion proteins in a single lab\", \"Does not establish the metabolic function of the compartmentalized complex\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Whether apicoplast PDH actually drives fatty acid synthesis and is essential was unresolved; direct deletion showed PDHE1A supplies carbon for de novo fatty acid biosynthesis and is required for apicoplast maintenance but dispensable in vivo via host lipid salvage.\",\n      \"evidence\": \"CRISPR/Cas9 deletion of pdh-e1\\u03b1, glucose metabolic labeling, fatty acid supplementation rescue, and mouse virulence assay\",\n      \"pmids\": [\"32341123\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of apicoplast loss upon deletion not resolved\", \"Enzymatic parameters of the PDHE1A subunit not defined\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"It was unclear whether apicoplast PDH provides a functionally distinct acetyl-CoA pool; multi-omics of mutants in other acetyl-CoA enzymes confirmed the PDH-derived pool is compartment-specific and dedicated to fatty acid synthesis.\",\n      \"evidence\": \"Multi-omics (acetylome, transcriptome, proteome, metabolome) of parasites lacking other acetyl-CoA-generating enzymes\",\n      \"pmids\": [\"32546260\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"PDH role inferred from complementary mutants rather than direct PDH KO in this study\", \"Does not resolve regulation of the PDH pool\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Whether parasite PDH is subject to kinase regulation was addressed pharmacologically; DCA increased PDH activity and perturbed organelle morphology, consistent with PDK-mediated regulation.\",\n      \"evidence\": \"PDH enzyme activity assay with dichloroacetate treatment and organelle morphology analysis\",\n      \"pmids\": [\"33408226\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Indirect pharmacological evidence with no direct genetic manipulation of PDHE1A\", \"Regulatory phosphorylation of PDHE1A not directly demonstrated\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PDHE1A is enzymatically regulated at the residue level and how its loss triggers apicoplast collapse remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct demonstration of PDHE1A phosphoregulation\", \"Structural and kinetic characterization of the subunit absent\", \"Mechanistic link between loss of fatty acid synthesis and apicoplast loss undefined\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004739\", \"supporting_discovery_ids\": [1, 3], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0020011\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006633\", \"supporting_discovery_ids\": [1, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0006086\", \"supporting_discovery_ids\": [1, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"Pyruvate dehydrogenase complex (apicoplast PDH)\"],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Deletion of pdh-e1\\u03b1 causes apicoplast loss and impaired growth but preserves mouse virulence via host fatty acid salvage\",\n      \"PDH activity is increased by dichloroacetate, consistent with regulation by PDK kinases\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_245670","name":"PDHE1A","product":"pyruvate dehydrogenase complex subunit PDH-E1Alpha","uniprot_acc":"S8ENF7","chromosome":"TGME49_chrXII","start_pos":2458250},{"strain":"GT1","gene_id":"TGGT1_245670","name":null,"product":"pyruvate dehydrogenase complex subunit PDH-E1Alpha","uniprot_acc":null,"chromosome":"TGGT1_chrXII","start_pos":2396583},{"strain":"RH88","gene_id":"TGRH88_060290","name":null,"product":"pyruvate dehydrogenase complex subunit PDH-E1Alpha","uniprot_acc":null,"chromosome":"CM023093","start_pos":2487671},{"strain":"VEG","gene_id":"TGVEG_245670","name":null,"product":"pyruvate dehydrogenase complex subunit PDH-E1Alpha","uniprot_acc":"B9QC91","chromosome":"TGVEG_chrXII","start_pos":2426961}]}