{"gene":"TG_240890","gene_symbol":"PFK1","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2022,"finding":"Toxoplasma gondii expresses both ATP-dependent (ATP-PFK, i.e. PFK1) and PPi-dependent phosphofructokinases (PPi-PFK) in the cytoplasm; deletion of ATP-PFK (PFK1) did not affect parasite proliferation or virulence, demonstrating it is dispensable for growth.","method":"Gene deletion / knockout with parasite growth and virulence assays","journal":"PLoS Pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean gene deletion with defined phenotypic readout (growth and virulence), single lab, two orthogonal readouts (in vitro proliferation and in vivo virulence)","pmids":["35104280"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"PFK1 (ATP-PFK) localizes to the cytoplasm of Toxoplasma gondii, as determined by localization studies showing both phosphofructokinases are cytoplasmic.","method":"Subcellular localization experiment (fractionation / imaging)","journal":"PLoS Pathogens","confidence":"Low","confidence_rationale":"Tier 3 / Weak — localization mentioned in abstract without detailed methodological description for PFK1 specifically, single lab","pmids":["35104280"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"In Toxoplasma gondii, PFK1 (ATP-dependent phosphofructokinase) is a cytoplasmic enzyme whose deletion does not impair parasite growth or virulence, indicating it is dispensable, in contrast to the essential PPi-dependent phosphofructokinase that maintains pyrophosphate homeostasis."},"narrative":{"mechanistic_narrative":"In Toxoplasma gondii, PFK1 is an ATP-dependent phosphofructokinase (ATP-PFK) expressed in the cytoplasm alongside a distinct PPi-dependent phosphofructokinase [PMID:35104280]. Genetic deletion of PFK1 does not impair parasite proliferation in vitro or virulence in vivo, establishing that PFK1 is dispensable for growth [PMID:35104280]. Beyond its cytoplasmic localization [PMID:35104280] and dispensability [PMID:35104280], no further mechanistic detail on PFK1 has been characterized in the available corpus.","teleology":[{"year":2022,"claim":"It was unknown whether the ATP-dependent phosphofructokinase contributes non-redundantly to Toxoplasma glycolysis and fitness; targeted deletion showed PFK1 is dispensable for both proliferation and virulence, establishing that ATP-PFK activity is not required for parasite growth.","evidence":"Gene deletion / knockout with in vitro proliferation and in vivo virulence assays in Toxoplasma gondii","pmids":["35104280"],"confidence":"Medium","gaps":["Does not test functional redundancy with the PPi-dependent phosphofructokinase (e.g. double-deletion or conditional depletion)","No direct enzymatic characterization of PFK1 activity","No metabolic flux measurement to confirm glycolytic contribution"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"The subcellular compartment of PFK1 was undefined; localization studies placed PFK1 in the cytoplasm, consistent with a role in cytosolic glycolysis.","evidence":"Subcellular localization experiment (fractionation / imaging) in Toxoplasma gondii","pmids":["35104280"],"confidence":"Low","gaps":["Localization reported without detailed methodology specific to PFK1","No co-localization or high-resolution imaging to exclude additional compartments"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":["Deletion of PFK1 (ATP-PFK) does not affect Toxoplasma gondii proliferation or virulence, indicating dispensability [#0].","PFK1 is expressed in the cytoplasm alongside a distinct PPi-dependent phosphofructokinase [#0, #1]."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"35104280","id":"PMC_35104280","title":"Essential role of pyrophosphate homeostasis mediated by the pyrophosphate-dependent phosphofructokinase in Toxoplasma gondii.","date":"2022","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/35104280","citation_count":18,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3004,"output_tokens":909,"usd":0.011324,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5831,"output_tokens":1904,"usd":0.038378,"stage2_stop_reason":"end_turn"},"total_usd":0.091798,"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\": 2022,\n      \"finding\": \"Toxoplasma gondii expresses both ATP-dependent (ATP-PFK, i.e. PFK1) and PPi-dependent phosphofructokinases (PPi-PFK) in the cytoplasm; deletion of ATP-PFK (PFK1) did not affect parasite proliferation or virulence, demonstrating it is dispensable for growth.\",\n      \"method\": \"Gene deletion / knockout with parasite growth and virulence assays\",\n      \"journal\": \"PLoS Pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean gene deletion with defined phenotypic readout (growth and virulence), single lab, two orthogonal readouts (in vitro proliferation and in vivo virulence)\",\n      \"pmids\": [\"35104280\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PFK1 (ATP-PFK) localizes to the cytoplasm of Toxoplasma gondii, as determined by localization studies showing both phosphofructokinases are cytoplasmic.\",\n      \"method\": \"Subcellular localization experiment (fractionation / imaging)\",\n      \"journal\": \"PLoS Pathogens\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — localization mentioned in abstract without detailed methodological description for PFK1 specifically, single lab\",\n      \"pmids\": [\"35104280\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"In Toxoplasma gondii, PFK1 (ATP-dependent phosphofructokinase) is a cytoplasmic enzyme whose deletion does not impair parasite growth or virulence, indicating it is dispensable, in contrast to the essential PPi-dependent phosphofructokinase that maintains pyrophosphate homeostasis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"In Toxoplasma gondii, PFK1 is an ATP-dependent phosphofructokinase (ATP-PFK) expressed in the cytoplasm alongside a distinct PPi-dependent phosphofructokinase [#0]. Genetic deletion of PFK1 does not impair parasite proliferation in vitro or virulence in vivo, establishing that PFK1 is dispensable for growth [#0]. Beyond its cytoplasmic localization [#1] and dispensability [#0], no further mechanistic detail on PFK1 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"It was unknown whether the ATP-dependent phosphofructokinase contributes non-redundantly to Toxoplasma glycolysis and fitness; targeted deletion showed PFK1 is dispensable for both proliferation and virulence, establishing that ATP-PFK activity is not required for parasite growth.\",\n      \"evidence\": \"Gene deletion / knockout with in vitro proliferation and in vivo virulence assays in Toxoplasma gondii\",\n      \"pmids\": [\n        \"35104280\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Does not test functional redundancy with the PPi-dependent phosphofructokinase (e.g. double-deletion or conditional depletion)\",\n        \"No direct enzymatic characterization of PFK1 activity\",\n        \"No metabolic flux measurement to confirm glycolytic contribution\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"The subcellular compartment of PFK1 was undefined; localization studies placed PFK1 in the cytoplasm, consistent with a role in cytosolic glycolysis.\",\n      \"evidence\": \"Subcellular localization experiment (fractionation / imaging) in Toxoplasma gondii\",\n      \"pmids\": [\n        \"35104280\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Localization reported without detailed methodology specific to PFK1\",\n        \"No co-localization or high-resolution imaging to exclude additional compartments\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PFK1 has any conditional or redundant role, its enzymatic kinetics, and its regulation remain unresolved in the available corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No enzymatic or kinetic characterization of PFK1\",\n        \"No test of redundancy with PPi-PFK under metabolic stress\",\n        \"No identified regulators or interaction partners\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0003872\",\n        \"supporting_discovery_ids\": [0],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0005737\",\n        \"supporting_discovery_ids\": [1],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0006096\",\n        \"supporting_discovery_ids\": [0],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Deletion of PFK1 (ATP-PFK) does not affect Toxoplasma gondii proliferation or virulence, indicating dispensability [#0].\",\n      \"PFK1 is expressed in the cytoplasm alongside a distinct PPi-dependent phosphofructokinase [#0, #1].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_240890","name":"PFK1","product":"6-phosphofructokinase","uniprot_acc":"A0A125YZ29","chromosome":"TGME49_chrVI","start_pos":1522758},{"strain":"GT1","gene_id":"TGGT1_240890","name":null,"product":"6-phosphofructokinase","uniprot_acc":null,"chromosome":"TGGT1_chrVI","start_pos":1494349},{"strain":"RH88","gene_id":"TGRH88_030270","name":null,"product":"6-phosphofructokinase","uniprot_acc":null,"chromosome":"CM023087","start_pos":2176511},{"strain":"VEG","gene_id":"TGVEG_240890","name":null,"product":"6-phosphofructokinase","uniprot_acc":"B6KFH7","chromosome":"TGVEG_chrVI","start_pos":1539750}]}