{"gene":"TG_272900","gene_symbol":"RAD51","run_date":"2026-09-08T14:08:30","timeline":{"discoveries":[{"year":2025,"finding":"T. gondii RAD51 is expressed in replicating tachyzoites and forms DNA damage foci, demonstrating it functions as the key recombinase in the homologous recombination repair (HRR) pathway to resolve DNA double-strand breaks arising during replication.","method":"Endogenous HA tagging via Auxin Inducible Degron (AID) system; immunofluorescence detection of damage foci","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization and functional tagging in endogenous locus, single lab, two complementary methods (AID knockdown + pharmacological inhibitor B02)","pmids":["40784138"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2025,"finding":"Auxin-induced knockdown of RAD51 disrupts tachyzoite replication synchronization, establishing that RAD51-mediated HRR is required for normal tachyzoite cell cycle progression.","method":"Auxin Inducible Degron (AID)-mediated conditional knockdown; cell cycle analysis","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional endogenous KD with defined replication phenotype, single lab, supported by orthogonal pharmacological inhibition","pmids":["40784138"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2025,"finding":"Pharmacological inhibition of RAD51 with inhibitor B02 (IC50 4.8 µM) causes S-phase arrest in tachyzoites and induces tachyzoite-to-bradyzoite differentiation with formation of small cyst-like structures, linking DNA replication stress to stage conversion.","method":"Pharmacological inhibition with small molecule B02; growth assay; cell cycle analysis; stage conversion assay","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pharmacological inhibition with quantified IC50, defined cell cycle arrest and stage-conversion phenotype, single lab, consistent with AID knockdown data","pmids":["40784138"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]}],"current_model":"Toxoplasma gondii RAD51 is the key recombinase of the homologous recombination repair pathway, forming DNA damage foci in replicating tachyzoites to resolve replication-associated DNA double-strand breaks; its loss (by AID-mediated knockdown or B02 inhibition) causes S-phase arrest, loss of replication synchrony, and induces tachyzoite-to-bradyzoite stage differentiation, indicating that RAD51-dependent genome maintenance suppresses stress-induced stage conversion."},"narrative":{"mechanistic_narrative":"In Toxoplasma gondii (strain RH), RAD51 is the key recombinase of the homologous recombination repair (HRR) pathway, expressed in replicating tachyzoites where it forms DNA damage foci to resolve DNA double-strand breaks that arise during replication [PMID:40784138]. Its activity is required for normal cell cycle progression: conditional AID-mediated knockdown disrupts tachyzoite replication synchronization [PMID:40784138], and pharmacological inhibition with B02 (IC50 4.8 µM) causes S-phase arrest [PMID:40784138]. Beyond genome maintenance, RAD51 loss couples replication stress to developmental fate, since B02 inhibition induces tachyzoite-to-bradyzoite differentiation with formation of small cyst-like structures — indicating that RAD51-dependent genome maintenance suppresses stress-induced stage conversion [PMID:40784138]. No further mechanistic detail on RAD51 partners, substrates, or the molecular basis of foci assembly has been characterized in the available corpus.","teleology":[{"year":2025,"claim":"Whether T. gondii possesses a functional HRR recombinase acting during replication was unknown; endogenous tagging showed RAD51 is expressed in replicating tachyzoites and assembles into DNA damage foci, establishing it as the key recombinase resolving replication-associated double-strand breaks.","evidence":"Endogenous HA tagging via AID system with immunofluorescence detection of damage foci in T. gondii RH tachyzoites","pmids":["40784138"],"confidence":"Medium","gaps":["No interacting partners, presynaptic filament components, or substrates identified","Molecular trigger and composition of the damage foci not defined","No structural model of the recombinase or its filament"],"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2025,"claim":"It was unclear whether HRR activity is required for parasite proliferation; conditional depletion showed RAD51 loss disrupts replication synchronization, establishing that RAD51-mediated HRR is needed for normal tachyzoite cell cycle progression.","evidence":"AID-mediated conditional knockdown with cell cycle analysis in T. gondii RH","pmids":["40784138"],"confidence":"Medium","gaps":["The specific cell cycle checkpoint engaged by RAD51 loss is not mapped","Whether the replication defect reflects unresolved DSBs versus a signaling role is not distinguished"],"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2025,"claim":"Whether replication stress could drive developmental conversion was unknown; pharmacological RAD51 inhibition caused S-phase arrest and induced tachyzoite-to-bradyzoite differentiation, linking genome maintenance failure to stress-induced stage conversion.","evidence":"Small-molecule inhibition with B02 (IC50 4.8 µM); growth, cell cycle, and stage conversion assays in T. gondii RH","pmids":["40784138"],"confidence":"Medium","gaps":["B02 off-target effects not excluded by genetic epistasis for the differentiation phenotype","Signaling pathway connecting S-phase arrest to bradyzoite conversion not defined","Whether cyst-like structures represent bona fide mature bradyzoites in vivo is untested"],"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":null,"claim":"The molecular interactors, upstream loaders, and downstream effectors that mediate RAD51 filament assembly and the link between replication stress and stage conversion remain undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No partner proteins or mediator/loader factors identified","Mechanism coupling S-phase arrest to bradyzoite differentiation unknown","No cross-strain comparison beyond RH"],"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":["RAD51 inhibition (B02, IC50 4.8 µM) induces tachyzoite-to-bradyzoite differentiation with small cyst-like structures, coupling genome maintenance to stage conversion [#2]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"40784138","id":"PMC_40784138","title":"Toxoplasma gondii RAD51 recombinase is required to overcome DNA replication stress and its inactivation leads to bradyzoite differentiation.","date":"2025","source":"DNA repair","url":"https://pubmed.ncbi.nlm.nih.gov/40784138","citation_count":1,"is_preprint":false},{"pmid":"40291705","id":"PMC_40291705","title":"Toxoplasma gondii RAD51 recombinase is required to overcome DNA replication stress and its inactivation leads to bradyzoite differentiation.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40291705","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3419,"output_tokens":839,"usd":0.011421,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5679,"output_tokens":2048,"usd":0.039797,"stage2_stop_reason":"end_turn"},"total_usd":0.051218,"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\": 2025,\n      \"finding\": \"T. gondii RAD51 is expressed in replicating tachyzoites and forms DNA damage foci, demonstrating it functions as the key recombinase in the homologous recombination repair (HRR) pathway to resolve DNA double-strand breaks arising during replication.\",\n      \"method\": \"Endogenous HA tagging via Auxin Inducible Degron (AID) system; immunofluorescence detection of damage foci\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization and functional tagging in endogenous locus, single lab, two complementary methods (AID knockdown + pharmacological inhibitor B02)\",\n      \"pmids\": [\"40784138\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Auxin-induced knockdown of RAD51 disrupts tachyzoite replication synchronization, establishing that RAD51-mediated HRR is required for normal tachyzoite cell cycle progression.\",\n      \"method\": \"Auxin Inducible Degron (AID)-mediated conditional knockdown; cell cycle analysis\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional endogenous KD with defined replication phenotype, single lab, supported by orthogonal pharmacological inhibition\",\n      \"pmids\": [\"40784138\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Pharmacological inhibition of RAD51 with inhibitor B02 (IC50 4.8 µM) causes S-phase arrest in tachyzoites and induces tachyzoite-to-bradyzoite differentiation with formation of small cyst-like structures, linking DNA replication stress to stage conversion.\",\n      \"method\": \"Pharmacological inhibition with small molecule B02; growth assay; cell cycle analysis; stage conversion assay\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pharmacological inhibition with quantified IC50, defined cell cycle arrest and stage-conversion phenotype, single lab, consistent with AID knockdown data\",\n      \"pmids\": [\"40784138\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    }\n  ],\n  \"current_model\": \"Toxoplasma gondii RAD51 is the key recombinase of the homologous recombination repair pathway, forming DNA damage foci in replicating tachyzoites to resolve replication-associated DNA double-strand breaks; its loss (by AID-mediated knockdown or B02 inhibition) causes S-phase arrest, loss of replication synchrony, and induces tachyzoite-to-bradyzoite stage differentiation, indicating that RAD51-dependent genome maintenance suppresses stress-induced stage conversion.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"In Toxoplasma gondii (strain RH), RAD51 is the key recombinase of the homologous recombination repair (HRR) pathway, expressed in replicating tachyzoites where it forms DNA damage foci to resolve DNA double-strand breaks that arise during replication [#0]. Its activity is required for normal cell cycle progression: conditional AID-mediated knockdown disrupts tachyzoite replication synchronization [#1], and pharmacological inhibition with B02 (IC50 4.8 µM) causes S-phase arrest [#2]. Beyond genome maintenance, RAD51 loss couples replication stress to developmental fate, since B02 inhibition induces tachyzoite-to-bradyzoite differentiation with formation of small cyst-like structures — indicating that RAD51-dependent genome maintenance suppresses stress-induced stage conversion [#2]. No further mechanistic detail on RAD51 partners, substrates, or the molecular basis of foci assembly has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether T. gondii possesses a functional HRR recombinase acting during replication was unknown; endogenous tagging showed RAD51 is expressed in replicating tachyzoites and assembles into DNA damage foci, establishing it as the key recombinase resolving replication-associated double-strand breaks.\",\n      \"evidence\": \"Endogenous HA tagging via AID system with immunofluorescence detection of damage foci in T. gondii RH tachyzoites\",\n      \"pmids\": [\"40784138\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No interacting partners, presynaptic filament components, or substrates identified\",\n        \"Molecular trigger and composition of the damage foci not defined\",\n        \"No structural model of the recombinase or its filament\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"It was unclear whether HRR activity is required for parasite proliferation; conditional depletion showed RAD51 loss disrupts replication synchronization, establishing that RAD51-mediated HRR is needed for normal tachyzoite cell cycle progression.\",\n      \"evidence\": \"AID-mediated conditional knockdown with cell cycle analysis in T. gondii RH\",\n      \"pmids\": [\"40784138\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The specific cell cycle checkpoint engaged by RAD51 loss is not mapped\",\n        \"Whether the replication defect reflects unresolved DSBs versus a signaling role is not distinguished\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether replication stress could drive developmental conversion was unknown; pharmacological RAD51 inhibition caused S-phase arrest and induced tachyzoite-to-bradyzoite differentiation, linking genome maintenance failure to stress-induced stage conversion.\",\n      \"evidence\": \"Small-molecule inhibition with B02 (IC50 4.8 µM); growth, cell cycle, and stage conversion assays in T. gondii RH\",\n      \"pmids\": [\"40784138\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"B02 off-target effects not excluded by genetic epistasis for the differentiation phenotype\",\n        \"Signaling pathway connecting S-phase arrest to bradyzoite conversion not defined\",\n        \"Whether cyst-like structures represent bona fide mature bradyzoites in vivo is untested\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular interactors, upstream loaders, and downstream effectors that mediate RAD51 filament assembly and the link between replication stress and stage conversion remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No partner proteins or mediator/loader factors identified\",\n        \"Mechanism coupling S-phase arrest to bradyzoite differentiation unknown\",\n        \"No cross-strain comparison beyond RH\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003697\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]},\n      {\"term_id\": \"GO:0000150\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0035861\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0000724\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]},\n      {\"term_id\": \"GO:0007049\", \"supporting_discovery_ids\": [1, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]}\n    ],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"RAD51 inhibition (B02, IC50 4.8 µM) induces tachyzoite-to-bradyzoite differentiation with small cyst-like structures, coupling genome maintenance to stage conversion [#2]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_272900","name":"RAD51","product":"DNA repair protein RAD51","uniprot_acc":"A0A125YQJ7","chromosome":"TGME49_chrVIII","start_pos":3719047},{"strain":"GT1","gene_id":"TGGT1_272900","name":null,"product":"putative DNA repair protein RAD51","uniprot_acc":null,"chromosome":"TGGT1_chrVIII","start_pos":3716460},{"strain":"RH88","gene_id":"TGRH88_078950","name":null,"product":"putative DNA repair protein RAD51","uniprot_acc":null,"chromosome":"CM023089","start_pos":8827920},{"strain":"VEG","gene_id":"TGVEG_272900","name":null,"product":"putative DNA repair protein RAD51","uniprot_acc":"B9PFU0","chromosome":"TGVEG_chrVIII","start_pos":3728588}]}