{"gene":"TG_295340","gene_symbol":"","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2020,"finding":"TGME49_295340 (RAD23, also annotated as TGGT1_295340), a UBL-UBA shuttle protein, localizes to the cytoplasm and nucleus of T. gondii and contributes to the degradation of ubiquitinylated proteins by escorting them to the proteasome; deletion of RAD23 (as part of a triple-gene knockout with DDI1 and DSK2) inhibited parasite growth, caused accumulation of ubiquitinylated proteins, and resulted in asynchronous cell division.","method":"Gene deletion (knockout), subcellular localization (cytoplasm/nucleus), ubiquitinylated protein accumulation assay, parasite growth assay, cell division phenotype analysis","journal":"FASEB Journal","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean KO with defined cellular phenotype (growth inhibition, ubiquitin accumulation, asynchronous division), but RAD23 was knocked out as part of a triple-gene KO, making it difficult to attribute individual contributions; single lab, single study","pmids":["32808330"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"GT1"}]}],"current_model":"TGME49_295340 (RAD23) is a UBL-UBA shuttle protein that localizes to the cytoplasm and nucleus of T. gondii and functions within the ubiquitin-proteasome system to escort ubiquitinylated proteins to the proteasome for degradation, with loss of this protein (together with DDI1 and DSK2) causing accumulation of ubiquitinylated proteins, impaired parasite growth, and asynchronous cell division."},"narrative":{"mechanistic_narrative":"TGME49_295340 (RAD23) is a UBL-UBA shuttle protein that operates within the ubiquitin-proteasome system of Toxoplasma gondii, escorting ubiquitinylated proteins to the proteasome for degradation [PMID:32808330]. It localizes to both the cytoplasm and nucleus [PMID:32808330]. Deletion of RAD23, carried out together with DDI1 and DSK2 in a triple-gene knockout, caused accumulation of ubiquitinylated proteins, inhibited parasite growth, and produced asynchronous cell division [PMID:32808330]. Because RAD23 was disrupted only as part of this triple knockout, its individual contribution to these phenotypes has not been isolated in the available corpus.","teleology":[{"year":2020,"claim":"Establishing whether RAD23 participates in proteasomal targeting in T. gondii, the finding showed it is a cytoplasmic and nuclear UBL-UBA shuttle protein whose loss impairs clearance of ubiquitinylated proteins, tying it to the parasite's protein degradation machinery.","evidence":"Gene deletion (triple KO with DDI1 and DSK2), subcellular localization, ubiquitinylated protein accumulation assay, growth and cell division phenotype analysis in T. gondii GT1","pmids":["32808330"],"confidence":"Medium","gaps":["RAD23 was deleted only within a triple KO, so its individual contribution to ubiquitin accumulation, growth inhibition, and asynchronous division is not separable","No direct demonstration of physical interaction with the proteasome or with ubiquitinylated cargo","No structural or domain-level dissection of the UBL and UBA functions"],"attribution":[{"species":"Toxoplasma gondii","strain":"GT1"}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["DDI1 (CO-DELETED IN TRIPLE KO) [#0]","DSK2 (CO-DELETED IN TRIPLE KO) [#0]"],"other_free_text":["Loss of RAD23 (in triple KO with DDI1 and DSK2) causes accumulation of ubiquitinylated proteins, growth inhibition, and asynchronous cell division [#0]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"32808330","id":"PMC_32808330","title":"Toxoplasma gondii UBL-UBA shuttle proteins contribute to the degradation of ubiquitinylated proteins and are important for synchronous cell division and virulence.","date":"2020","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/32808330","citation_count":24,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4012,"output_tokens":1136,"usd":0.014538,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6117,"output_tokens":2580,"usd":0.047543,"stage2_stop_reason":"end_turn"},"total_usd":0.102267,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","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\": 2020,\n      \"finding\": \"TGME49_295340 (RAD23, also annotated as TGGT1_295340), a UBL-UBA shuttle protein, localizes to the cytoplasm and nucleus of T. gondii and contributes to the degradation of ubiquitinylated proteins by escorting them to the proteasome; deletion of RAD23 (as part of a triple-gene knockout with DDI1 and DSK2) inhibited parasite growth, caused accumulation of ubiquitinylated proteins, and resulted in asynchronous cell division.\",\n      \"method\": \"Gene deletion (knockout), subcellular localization (cytoplasm/nucleus), ubiquitinylated protein accumulation assay, parasite growth assay, cell division phenotype analysis\",\n      \"journal\": \"FASEB Journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean KO with defined cellular phenotype (growth inhibition, ubiquitin accumulation, asynchronous division), but RAD23 was knocked out as part of a triple-gene KO, making it difficult to attribute individual contributions; single lab, single study\",\n      \"pmids\": [\"32808330\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"GT1\"}\n      ]\n    }\n  ],\n  \"current_model\": \"TGME49_295340 (RAD23) is a UBL-UBA shuttle protein that localizes to the cytoplasm and nucleus of T. gondii and functions within the ubiquitin-proteasome system to escort ubiquitinylated proteins to the proteasome for degradation, with loss of this protein (together with DDI1 and DSK2) causing accumulation of ubiquitinylated proteins, impaired parasite growth, and asynchronous cell division.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TGME49_295340 (RAD23) is a UBL-UBA shuttle protein that operates within the ubiquitin-proteasome system of Toxoplasma gondii, escorting ubiquitinylated proteins to the proteasome for degradation [#0]. It localizes to both the cytoplasm and nucleus [#0]. Deletion of RAD23, carried out together with DDI1 and DSK2 in a triple-gene knockout, caused accumulation of ubiquitinylated proteins, inhibited parasite growth, and produced asynchronous cell division [#0]. Because RAD23 was disrupted only as part of this triple knockout, its individual contribution to these phenotypes has not been isolated in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2020,\n      \"claim\": \"Establishing whether RAD23 participates in proteasomal targeting in T. gondii, the finding showed it is a cytoplasmic and nuclear UBL-UBA shuttle protein whose loss impairs clearance of ubiquitinylated proteins, tying it to the parasite's protein degradation machinery.\",\n      \"evidence\": \"Gene deletion (triple KO with DDI1 and DSK2), subcellular localization, ubiquitinylated protein accumulation assay, growth and cell division phenotype analysis in T. gondii GT1\",\n      \"pmids\": [\n        \"32808330\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"RAD23 was deleted only within a triple KO, so its individual contribution to ubiquitin accumulation, growth inhibition, and asynchronous division is not separable\",\n        \"No direct demonstration of physical interaction with the proteasome or with ubiquitinylated cargo\",\n        \"No structural or domain-level dissection of the UBL and UBA functions\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"GT1\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The specific, non-redundant role of RAD23 relative to DDI1 and DSK2, and its direct binding partners, remain undetermined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-gene RAD23 knockout phenotype not reported\",\n        \"Direct proteasome and ubiquitin-cargo interactions not tested\",\n        \"No independent replication beyond the single study\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"GT1\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0043130\",\n        \"supporting_discovery_ids\": [0],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"GT1\"\n          }\n        ]\n      }\n    ],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0005737\",\n        \"supporting_discovery_ids\": [0],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"GT1\"\n          }\n        ]\n      },\n      {\n        \"term_id\": \"GO:0005634\",\n        \"supporting_discovery_ids\": [0],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"GT1\"\n          }\n        ]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0043161\",\n        \"supporting_discovery_ids\": [0],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"GT1\"\n          }\n        ]\n      }\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"DDI1 (co-deleted in triple KO) [#0]\",\n      \"DSK2 (co-deleted in triple KO) [#0]\"\n    ],\n    \"other_free_text\": [\n      \"Loss of RAD23 (in triple KO with DDI1 and DSK2) causes accumulation of ubiquitinylated proteins, growth inhibition, and asynchronous cell division [#0]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_295340","name":null,"product":"UV excision repair protein Rad23 protein","uniprot_acc":"A0A125YYY9","chromosome":"TGME49_chrIa","start_pos":1812981},{"strain":"GT1","gene_id":"TGGT1_295340","name":null,"product":"UV excision repair protein Rad23 protein","uniprot_acc":null,"chromosome":"TGGT1_chrIa","start_pos":1797323},{"strain":"RH88","gene_id":"TGRH88_020670","name":null,"product":"UV excision repair protein Rad23 protein","uniprot_acc":null,"chromosome":"CM023081","start_pos":1823886},{"strain":"VEG","gene_id":"TGVEG_295340","name":null,"product":"UV excision repair protein Rad23 protein","uniprot_acc":"A0A0F7UT30","chromosome":"TGVEG_chrIa","start_pos":1829965}]}