{"gene":"TG_247195","gene_symbol":"RDF1","run_date":"2026-09-08T12:58:25","timeline":{"discoveries":[{"year":2022,"finding":"RDF1 (previously annotated as MIC15) is a thrombospondin-related protein with a C-terminal transmembrane domain and short cytoplasmic tail that localizes to a diffuse punctate compartment distinct from known subcellular organelles in T. gondii tachyzoites.","method":"Immunofluorescence analysis of T. gondii tachyzoites","journal":"Frontiers in microbiology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization by immunofluorescence in a single study, with domain characterization; no functional validation of the localization itself","pmids":["35756016"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"Conditional knockdown of RDF1 dramatically reduces host cell invasion without affecting parasite gliding motility, host cell attachment, replication, or egress, placing RDF1 specifically in the invasion step.","method":"Conditional knockdown (inducible knockdown system) with phenotypic assays for motility, attachment, invasion, replication, and egress","journal":"Frontiers in microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean conditional KO with multiple defined phenotypic readouts in a single lab study","pmids":["35756016"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"RDF1 depletion does not impair microneme exocytosis but heavily impairs rhoptry discharge, demonstrating that RDF1 is specifically required for rhoptry secretion during invasion.","method":"Conditional knockdown combined with rhoptry and microneme secretion assays","journal":"Frontiers in microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional loss-of-function with organelle-specific secretion assays distinguishing microneme vs. rhoptry exocytosis; single lab","pmids":["35756016"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"Spontaneous upregulation of the paralogous gene RDF2 in RDF1 knockdown parasites grown under constant RDF1 repression reverses the rhoptry secretion defect, revealing a compensatory mechanism and functional redundancy between RDF1 and RDF2.","method":"Conditional knockdown with long-term culture and monitoring of RDF2 expression and rhoptry secretion rescue","journal":"Frontiers in microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic compensation observed in a single lab with functional secretion readout; spontaneous upregulation confirmed by gene expression monitoring","pmids":["35756016"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"RDF1 and RDF2 are paralogous thrombospondin-related proteins exclusive to the Coccidia class of apicomplexan parasites, sharing a C-terminal transmembrane domain followed by a short cytoplasmic tail.","method":"Sequence analysis and phylogenetic comparison across apicomplexan parasites","journal":"Frontiers in microbiology","confidence":"Low","confidence_rationale":"Tier 4 / Moderate — computational/sequence-based classification across species; no in vitro functional validation of the domain structure","pmids":["35756016"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"RDF1 is a Coccidia-specific thrombospondin-related transmembrane protein that localizes to a punctate compartment in T. gondii tachyzoites and is specifically required for rhoptry discharge (but not microneme exocytosis) during host cell invasion, with its paralog RDF2 able to compensate for its loss through spontaneous upregulation."},"narrative":{"mechanistic_narrative":"RDF1 (formerly annotated MIC15) is a Coccidia-specific thrombospondin-related transmembrane protein that functions specifically at the host cell invasion step of the Toxoplasma gondii tachyzoite lytic cycle [PMID:35756016]. The protein carries a C-terminal transmembrane domain and short cytoplasmic tail and localizes to a diffuse punctate compartment distinct from known subcellular organelles [PMID:35756016]. Conditional depletion of RDF1 dramatically reduces invasion while leaving gliding motility, host attachment, replication, and egress intact, and mechanistically this defect maps to impaired rhoptry discharge rather than microneme exocytosis [PMID:35756016]. RDF1 is functionally redundant with its paralog RDF2: spontaneous upregulation of RDF2 under constant RDF1 repression reverses the rhoptry secretion defect [PMID:35756016]. Beyond these findings, the molecular partners and biochemical mechanism by which RDF1 promotes rhoptry discharge have not been characterized in the available corpus.","teleology":[{"year":2022,"claim":"Establishing where a previously misannotated thrombospondin-related protein resides defined RDF1 as a distinct compartment-associated transmembrane protein rather than a canonical microneme component.","evidence":"Immunofluorescence and domain analysis of T. gondii tachyzoites (re-annotating MIC15 as RDF1)","pmids":["35756016"],"confidence":"Medium","gaps":["The identity of the punctate compartment is undefined","No interacting partners at this compartment identified","Domain architecture not functionally dissected"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"Conditional knockdown resolved which stage of the lytic cycle depends on RDF1, isolating its role to host cell invasion rather than motility, attachment, replication, or egress.","evidence":"Inducible knockdown with phenotypic assays across the lytic cycle in T. gondii","pmids":["35756016"],"confidence":"Medium","gaps":["Does not reveal the molecular event RDF1 controls within invasion","Single-lab study without independent replication"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"Organelle-specific secretion assays pinpointed the invasion defect to rhoptry discharge, distinguishing RDF1's role from microneme exocytosis.","evidence":"Conditional knockdown coupled to rhoptry and microneme secretion assays in T. gondii","pmids":["35756016"],"confidence":"Medium","gaps":["Mechanism linking RDF1 to rhoptry discharge unknown","Whether RDF1 acts directly on rhoptry machinery or upstream is unresolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"Long-term repression revealed that spontaneous upregulation of the paralog RDF2 rescues the rhoptry secretion defect, establishing functional redundancy between RDF1 and RDF2.","evidence":"Conditional knockdown with long-term culture, RDF2 expression monitoring, and rhoptry secretion rescue in T. gondii","pmids":["35756016"],"confidence":"Medium","gaps":["Regulatory basis of RDF2 upregulation unknown","Whether RDF1 and RDF2 act at the same molecular step or through parallel routes is untested"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"The molecular mechanism by which RDF1 promotes rhoptry discharge, its interacting partners, and the identity of its punctate compartment remain unknown.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No binding partners or substrates identified","No structural model","The punctate compartment remains unassigned to a known organelle"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["RDF2 (PARALOG; FUNCTIONALLY REDUNDANT, COMPENSATES UPON RDF1 LOSS)"],"other_free_text":["Thrombospondin-related protein with a C-terminal transmembrane domain and short cytoplasmic tail [#0, #4]","Coccidia-specific; paralogous with RDF2, both exclusive to the Coccidia class of apicomplexan parasites [#4]","Localizes to a diffuse punctate compartment distinct from known subcellular organelles [#0]","Specifically required for rhoptry discharge but dispensable for microneme exocytosis during host cell invasion [#2]","Previously annotated as MIC15 [#0]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"35756016","id":"PMC_35756016","title":"Functional Characterization of the Thrombospondin-Related Paralogous Proteins Rhoptry Discharge Factors 1 and 2 Unveils Phenotypic Plasticity in Toxoplasma gondii Rhoptry Exocytosis.","date":"2022","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/35756016","citation_count":11,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3088,"output_tokens":1193,"usd":0.013579,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6193,"output_tokens":2010,"usd":0.040607,"stage2_stop_reason":"end_turn"},"total_usd":0.054186,"stage1_batch_id":"msgbatch_01TEPNZ4MCzJ7xtsNwosiDRk","stage2_batch_id":"msgbatch_01FQShM7n1sfCr4pWTDShmki","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2022,\n      \"finding\": \"RDF1 (previously annotated as MIC15) is a thrombospondin-related protein with a C-terminal transmembrane domain and short cytoplasmic tail that localizes to a diffuse punctate compartment distinct from known subcellular organelles in T. gondii tachyzoites.\",\n      \"method\": \"Immunofluorescence analysis of T. gondii tachyzoites\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization by immunofluorescence in a single study, with domain characterization; no functional validation of the localization itself\",\n      \"pmids\": [\"35756016\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Conditional knockdown of RDF1 dramatically reduces host cell invasion without affecting parasite gliding motility, host cell attachment, replication, or egress, placing RDF1 specifically in the invasion step.\",\n      \"method\": \"Conditional knockdown (inducible knockdown system) with phenotypic assays for motility, attachment, invasion, replication, and egress\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean conditional KO with multiple defined phenotypic readouts in a single lab study\",\n      \"pmids\": [\"35756016\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RDF1 depletion does not impair microneme exocytosis but heavily impairs rhoptry discharge, demonstrating that RDF1 is specifically required for rhoptry secretion during invasion.\",\n      \"method\": \"Conditional knockdown combined with rhoptry and microneme secretion assays\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional loss-of-function with organelle-specific secretion assays distinguishing microneme vs. rhoptry exocytosis; single lab\",\n      \"pmids\": [\"35756016\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Spontaneous upregulation of the paralogous gene RDF2 in RDF1 knockdown parasites grown under constant RDF1 repression reverses the rhoptry secretion defect, revealing a compensatory mechanism and functional redundancy between RDF1 and RDF2.\",\n      \"method\": \"Conditional knockdown with long-term culture and monitoring of RDF2 expression and rhoptry secretion rescue\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic compensation observed in a single lab with functional secretion readout; spontaneous upregulation confirmed by gene expression monitoring\",\n      \"pmids\": [\"35756016\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RDF1 and RDF2 are paralogous thrombospondin-related proteins exclusive to the Coccidia class of apicomplexan parasites, sharing a C-terminal transmembrane domain followed by a short cytoplasmic tail.\",\n      \"method\": \"Sequence analysis and phylogenetic comparison across apicomplexan parasites\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Moderate — computational/sequence-based classification across species; no in vitro functional validation of the domain structure\",\n      \"pmids\": [\"35756016\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"RDF1 is a Coccidia-specific thrombospondin-related transmembrane protein that localizes to a punctate compartment in T. gondii tachyzoites and is specifically required for rhoptry discharge (but not microneme exocytosis) during host cell invasion, with its paralog RDF2 able to compensate for its loss through spontaneous upregulation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RDF1 (formerly annotated MIC15) is a Coccidia-specific thrombospondin-related transmembrane protein that functions specifically at the host cell invasion step of the Toxoplasma gondii tachyzoite lytic cycle [#0, #1]. The protein carries a C-terminal transmembrane domain and short cytoplasmic tail and localizes to a diffuse punctate compartment distinct from known subcellular organelles [#0]. Conditional depletion of RDF1 dramatically reduces invasion while leaving gliding motility, host attachment, replication, and egress intact, and mechanistically this defect maps to impaired rhoptry discharge rather than microneme exocytosis [#1, #2]. RDF1 is functionally redundant with its paralog RDF2: spontaneous upregulation of RDF2 under constant RDF1 repression reverses the rhoptry secretion defect [#3]. Beyond these findings, the molecular partners and biochemical mechanism by which RDF1 promotes rhoptry discharge have not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Establishing where a previously misannotated thrombospondin-related protein resides defined RDF1 as a distinct compartment-associated transmembrane protein rather than a canonical microneme component.\",\n      \"evidence\": \"Immunofluorescence and domain analysis of T. gondii tachyzoites (re-annotating MIC15 as RDF1)\",\n      \"pmids\": [\"35756016\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The identity of the punctate compartment is undefined\", \"No interacting partners at this compartment identified\", \"Domain architecture not functionally dissected\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Conditional knockdown resolved which stage of the lytic cycle depends on RDF1, isolating its role to host cell invasion rather than motility, attachment, replication, or egress.\",\n      \"evidence\": \"Inducible knockdown with phenotypic assays across the lytic cycle in T. gondii\",\n      \"pmids\": [\"35756016\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not reveal the molecular event RDF1 controls within invasion\", \"Single-lab study without independent replication\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Organelle-specific secretion assays pinpointed the invasion defect to rhoptry discharge, distinguishing RDF1's role from microneme exocytosis.\",\n      \"evidence\": \"Conditional knockdown coupled to rhoptry and microneme secretion assays in T. gondii\",\n      \"pmids\": [\"35756016\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking RDF1 to rhoptry discharge unknown\", \"Whether RDF1 acts directly on rhoptry machinery or upstream is unresolved\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Long-term repression revealed that spontaneous upregulation of the paralog RDF2 rescues the rhoptry secretion defect, establishing functional redundancy between RDF1 and RDF2.\",\n      \"evidence\": \"Conditional knockdown with long-term culture, RDF2 expression monitoring, and rhoptry secretion rescue in T. gondii\",\n      \"pmids\": [\"35756016\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Regulatory basis of RDF2 upregulation unknown\", \"Whether RDF1 and RDF2 act at the same molecular step or through parallel routes is untested\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular mechanism by which RDF1 promotes rhoptry discharge, its interacting partners, and the identity of its punctate compartment remain unknown.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No binding partners or substrates identified\", \"No structural model\", \"The punctate compartment remains unassigned to a known organelle\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0044409\", \"supporting_discovery_ids\": [1, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RDF2 (paralog; functionally redundant, compensates upon RDF1 loss)\"],\n    \"other_free_text\": [\n      \"Thrombospondin-related protein with a C-terminal transmembrane domain and short cytoplasmic tail [#0, #4]\",\n      \"Coccidia-specific; paralogous with RDF2, both exclusive to the Coccidia class of apicomplexan parasites [#4]\",\n      \"Localizes to a diffuse punctate compartment distinct from known subcellular organelles [#0]\",\n      \"Specifically required for rhoptry discharge but dispensable for microneme exocytosis during host cell invasion [#2]\",\n      \"Previously annotated as MIC15 [#0]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_247195","name":"RDF1","product":"rhoptry discharge factor RDF1","uniprot_acc":"S8G9F5","chromosome":"TGME49_chrXII","start_pos":3144686},{"strain":"GT1","gene_id":"TGGT1_247195","name":null,"product":"microneme protein MIC15","uniprot_acc":null,"chromosome":"TGGT1_chrXII","start_pos":3076266},{"strain":"RH88","gene_id":"TGRH88_061300","name":null,"product":"microneme protein MIC15","uniprot_acc":null,"chromosome":"CM023093","start_pos":3197636},{"strain":"VEG","gene_id":"TGVEG_247195","name":null,"product":"microneme protein MIC15","uniprot_acc":"V5BFN0","chromosome":"TGVEG_chrXII","start_pos":3113571}]}