{"gene":"TG_312050","gene_symbol":"RAB2","run_date":"2026-09-08T15:15:13","timeline":{"discoveries":[{"year":2024,"finding":"TgTBC9, a protozoan-specific TBC domain-containing protein localized to the endoplasmic reticulum, acts as a GTPase-activating protein (GAP) for TgRab2; immunoprecipitation and yeast two-hybrid analyses show TgTBC9 preferentially binds Rab2, and the conserved dual-finger active site in the TBC domain is required for GAP function, indicating the TBC9–Rab2 pair controls ER morphology and vesicular trafficking.","method":"Immunoprecipitation, yeast two-hybrid, auxin-inducible degron knockdown, active-site mutagenesis (dual-finger motif), fluorescence localization","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding shown by two orthogonal methods (Co-IP and Y2H), functional validation by AID knockdown with defined phenotype, active-site mutagenesis confirming GAP catalytic requirement, replicated across two independent labs (PMID:38713739 and PMID:38762629)","pmids":["38713739"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"finding":"Pull-down assays demonstrate a direct protein–protein interaction between TBC9 and Rab2 (as well as Rab11A and Rab11B), supporting a role for TBC9 in regulating early vesicular transport and daughter inner membrane complex (IMC) formation via these Rab GTPases.","method":"Pull-down assay, fluorescence localization, auxin-inducible degron knockdown","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single pull-down method for binding, but replicated finding across two independent labs; phenotypic consequence (ER/Golgi distribution defects, IMC formation defects) documented by orthogonal localization experiments","pmids":["38762629"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"finding":"TgTBC9 directly binds Rab2 (by immunoprecipitation and yeast two-hybrid) and the TBC9–Rab2 pair controls ER-to-Golgi traffic in T. gondii; knockdown of TgTBC9 disrupts ER and Golgi organization, consistent with loss of Rab2 GAP regulation at this trafficking step.","method":"Immunoprecipitation, yeast two-hybrid, auxin-inducible degron knockdown, fluorescence localization","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two orthogonal binding methods (Co-IP and Y2H) plus functional knockdown phenotype, but preprint version of data later peer-reviewed in PMID:38713739","pmids":["37398139"],"is_preprint":true,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"Toxoplasma gondii Rab2 is a Rab GTPase that operates in early secretory/vesicular trafficking (ER-to-Golgi pathway and daughter IMC formation), and its GTPase activity is regulated by the ER-localized GAP protein TgTBC9, which binds Rab2 directly (demonstrated by Co-IP and yeast two-hybrid) and requires its conserved dual-finger active site to exert GAP function."},"narrative":{"mechanistic_narrative":"Toxoplasma gondii Rab2 is a Rab GTPase that functions in early secretory and vesicular trafficking, specifically the ER-to-Golgi transport pathway [PMID:38713739, PMID:37398139]. Its GTPase cycle is controlled by TgTBC9, a protozoan-specific TBC domain-containing GTPase-activating protein (GAP) localized to the endoplasmic reticulum, which preferentially and directly binds Rab2 and requires the conserved dual-finger active site of its TBC domain for GAP activity [PMID:38713739]. Loss of TgTBC9 disrupts ER and Golgi organization, consistent with dysregulated Rab2 at this trafficking step [PMID:38713739, PMID:37398139], and TBC9 additionally engages Rab11A and Rab11B, linking this regulatory node to daughter inner membrane complex (IMC) formation [PMID:38762629]. Beyond its regulation by TgTBC9 in the secretory pathway, no further mechanistic detail on Rab2 effectors, nucleotide-exchange factors, or trafficking cargo has been characterized in the available corpus.","teleology":[{"year":2023,"claim":"It was unknown which regulator controls the Rab2 GTPase cycle in Toxoplasma; identifying a direct binding partner established TgTBC9 as a candidate GAP governing ER-to-Golgi traffic.","evidence":"Immunoprecipitation and yeast two-hybrid binding plus auxin-inducible degron knockdown with fluorescence localization in T. gondii (preprint)","pmids":["37398139"],"confidence":"Medium","gaps":["Preprint version later peer-reviewed","Catalytic GAP requirement not yet demonstrated at this stage","Effect on Rab2 nucleotide state not directly measured"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"claim":"Whether TgTBC9 acts catalytically on Rab2 rather than merely binding it was unresolved; active-site mutagenesis showed the conserved dual-finger motif is required for GAP function, establishing TgTBC9 as a bona fide Rab2 GAP controlling ER morphology and vesicular trafficking.","evidence":"Reciprocal Co-IP and yeast two-hybrid binding, auxin-inducible degron knockdown, and dual-finger active-site mutagenesis in T. gondii","pmids":["38713739"],"confidence":"High","gaps":["Direct measurement of Rab2 GTP hydrolysis acceleration in vitro not reported","Downstream Rab2 effectors unidentified","Cargo transiting the Rab2-dependent step not defined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"claim":"It was unclear whether TgTBC9 acts solely on Rab2; pull-down analysis showed it also directly binds Rab11A and Rab11B, extending its regulatory role to daughter IMC formation alongside early vesicular transport.","evidence":"Pull-down assay, fluorescence localization, and auxin-inducible degron knockdown in T. gondii","pmids":["38762629"],"confidence":"Medium","gaps":["Single binding method (pull-down) for the interactions","Relative preference among Rab2/Rab11A/Rab11B not quantified","GAP catalytic activity toward Rab11A/B not tested"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"The Rab2 effectors, guanine nucleotide-exchange factor, membrane cargo, and the biochemical kinetics of TgTBC9-stimulated GTP hydrolysis remain undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No Rab2 downstream effector identified","No GEF for Rab2 characterized","In vitro GAP kinetics not measured"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["TGTBC9 (ER-LOCALIZED TBC-DOMAIN GAP; DIRECT BINDING PARTNER AND GAP FOR RAB2)"],"other_free_text":["TgTBC9 also directly binds Rab11A and Rab11B, linking Rab regulation to daughter inner membrane complex (IMC) formation [#1]","The conserved dual-finger active site of the TgTBC9 TBC domain is required for GAP function toward Rab2 [#0]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"38713739","id":"PMC_38713739","title":"Systematic characterization of all Toxoplasma gondii TBC domain-containing proteins identifies an essential regulator of Rab2 in the secretory pathway.","date":"2024","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/38713739","citation_count":10,"is_preprint":false},{"pmid":"38762629","id":"PMC_38762629","title":"TBC9, an essential TBC-domain protein, regulates early vesicular transport and IMC formation in Toxoplasma gondii.","date":"2024","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/38762629","citation_count":5,"is_preprint":false},{"pmid":"37398139","id":"PMC_37398139","title":"Toxoplasma gondii encodes an array of TBC-domain containing proteins including an essential regulator that targets Rab2 in the secretory pathway.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37398139","citation_count":3,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4016,"output_tokens":1013,"usd":0.013621,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5873,"output_tokens":2085,"usd":0.040745,"stage2_stop_reason":"end_turn"},"total_usd":0.054366,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2024,\n      \"finding\": \"TgTBC9, a protozoan-specific TBC domain-containing protein localized to the endoplasmic reticulum, acts as a GTPase-activating protein (GAP) for TgRab2; immunoprecipitation and yeast two-hybrid analyses show TgTBC9 preferentially binds Rab2, and the conserved dual-finger active site in the TBC domain is required for GAP function, indicating the TBC9–Rab2 pair controls ER morphology and vesicular trafficking.\",\n      \"method\": \"Immunoprecipitation, yeast two-hybrid, auxin-inducible degron knockdown, active-site mutagenesis (dual-finger motif), fluorescence localization\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding shown by two orthogonal methods (Co-IP and Y2H), functional validation by AID knockdown with defined phenotype, active-site mutagenesis confirming GAP catalytic requirement, replicated across two independent labs (PMID:38713739 and PMID:38762629)\",\n      \"pmids\": [\"38713739\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Pull-down assays demonstrate a direct protein–protein interaction between TBC9 and Rab2 (as well as Rab11A and Rab11B), supporting a role for TBC9 in regulating early vesicular transport and daughter inner membrane complex (IMC) formation via these Rab GTPases.\",\n      \"method\": \"Pull-down assay, fluorescence localization, auxin-inducible degron knockdown\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single pull-down method for binding, but replicated finding across two independent labs; phenotypic consequence (ER/Golgi distribution defects, IMC formation defects) documented by orthogonal localization experiments\",\n      \"pmids\": [\"38762629\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TgTBC9 directly binds Rab2 (by immunoprecipitation and yeast two-hybrid) and the TBC9–Rab2 pair controls ER-to-Golgi traffic in T. gondii; knockdown of TgTBC9 disrupts ER and Golgi organization, consistent with loss of Rab2 GAP regulation at this trafficking step.\",\n      \"method\": \"Immunoprecipitation, yeast two-hybrid, auxin-inducible degron knockdown, fluorescence localization\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two orthogonal binding methods (Co-IP and Y2H) plus functional knockdown phenotype, but preprint version of data later peer-reviewed in PMID:38713739\",\n      \"pmids\": [\"37398139\"],\n      \"is_preprint\": true,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"Toxoplasma gondii Rab2 is a Rab GTPase that operates in early secretory/vesicular trafficking (ER-to-Golgi pathway and daughter IMC formation), and its GTPase activity is regulated by the ER-localized GAP protein TgTBC9, which binds Rab2 directly (demonstrated by Co-IP and yeast two-hybrid) and requires its conserved dual-finger active site to exert GAP function.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"Toxoplasma gondii Rab2 is a Rab GTPase that functions in early secretory and vesicular trafficking, specifically the ER-to-Golgi transport pathway [#0, #2]. Its GTPase cycle is controlled by TgTBC9, a protozoan-specific TBC domain-containing GTPase-activating protein (GAP) localized to the endoplasmic reticulum, which preferentially and directly binds Rab2 and requires the conserved dual-finger active site of its TBC domain for GAP activity [#0]. Loss of TgTBC9 disrupts ER and Golgi organization, consistent with dysregulated Rab2 at this trafficking step [#0, #2], and TBC9 additionally engages Rab11A and Rab11B, linking this regulatory node to daughter inner membrane complex (IMC) formation [#1]. Beyond its regulation by TgTBC9 in the secretory pathway, no further mechanistic detail on Rab2 effectors, nucleotide-exchange factors, or trafficking cargo has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"It was unknown which regulator controls the Rab2 GTPase cycle in Toxoplasma; identifying a direct binding partner established TgTBC9 as a candidate GAP governing ER-to-Golgi traffic.\",\n      \"evidence\": \"Immunoprecipitation and yeast two-hybrid binding plus auxin-inducible degron knockdown with fluorescence localization in T. gondii (preprint)\",\n      \"pmids\": [\"37398139\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint version later peer-reviewed\", \"Catalytic GAP requirement not yet demonstrated at this stage\", \"Effect on Rab2 nucleotide state not directly measured\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Whether TgTBC9 acts catalytically on Rab2 rather than merely binding it was unresolved; active-site mutagenesis showed the conserved dual-finger motif is required for GAP function, establishing TgTBC9 as a bona fide Rab2 GAP controlling ER morphology and vesicular trafficking.\",\n      \"evidence\": \"Reciprocal Co-IP and yeast two-hybrid binding, auxin-inducible degron knockdown, and dual-finger active-site mutagenesis in T. gondii\",\n      \"pmids\": [\"38713739\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct measurement of Rab2 GTP hydrolysis acceleration in vitro not reported\", \"Downstream Rab2 effectors unidentified\", \"Cargo transiting the Rab2-dependent step not defined\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"It was unclear whether TgTBC9 acts solely on Rab2; pull-down analysis showed it also directly binds Rab11A and Rab11B, extending its regulatory role to daughter IMC formation alongside early vesicular transport.\",\n      \"evidence\": \"Pull-down assay, fluorescence localization, and auxin-inducible degron knockdown in T. gondii\",\n      \"pmids\": [\"38762629\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single binding method (pull-down) for the interactions\", \"Relative preference among Rab2/Rab11A/Rab11B not quantified\", \"GAP catalytic activity toward Rab11A/B not tested\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The Rab2 effectors, guanine nucleotide-exchange factor, membrane cargo, and the biochemical kinetics of TgTBC9-stimulated GTP hydrolysis remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No Rab2 downstream effector identified\", \"No GEF for Rab2 characterized\", \"In vitro GAP kinetics not measured\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [0, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [1, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006888\", \"supporting_discovery_ids\": [0, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0016192\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"TgTBC9 (ER-localized TBC-domain GAP; direct binding partner and GAP for Rab2)\"\n    ],\n    \"other_free_text\": [\n      \"TgTBC9 also directly binds Rab11A and Rab11B, linking Rab regulation to daughter inner membrane complex (IMC) formation [#1]\",\n      \"The conserved dual-finger active site of the TgTBC9 TBC domain is required for GAP function toward Rab2 [#0]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_312050","name":"RAB2","product":"ras-related protein RAB2","uniprot_acc":"A0A125YL14","chromosome":"TGME49_chrXI","start_pos":2396295},{"strain":"GT1","gene_id":"TGGT1_312050","name":null,"product":"putative small GTPase Rab2","uniprot_acc":null,"chromosome":"TGGT1_chrXI","start_pos":2359586},{"strain":"RH88","gene_id":"TGRH88_051300","name":null,"product":"putative small GTPase Rab2","uniprot_acc":null,"chromosome":"CM023092","start_pos":2445253},{"strain":"VEG","gene_id":"TGVEG_312050","name":null,"product":"putative small GTPase Rab2","uniprot_acc":"B9PK50","chromosome":"TGVEG_chrXI","start_pos":2408541}]}