{"gene":"TG_246610","gene_symbol":"","run_date":"2026-09-08T12:58:25","timeline":{"discoveries":[{"year":2021,"finding":"TgVAMP4-2 is an R-SNARE localized to the outermost membrane of the apicoplast in Toxoplasma gondii, and its conditional knockout blocked import of nucleus-encoded apicoplast-targeted proteins (TgCPN60, TgACP, TgATrx2, TgATrx1) into the apicoplast and interfered with targeting of TgAPT1 and TgFtsH1 to the outermost apicoplast membrane, establishing that TgVAMP4-2 functions in vesicular trafficking required for protein import into this secondary endosymbiotic organelle.","method":"Conditional knockout (conditional ablation), subcellular localization analysis, protein import assay","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 / Moderate — conditional knockout with multiple specific protein import readouts, direct localization determination, single lab but multiple orthogonal functional assays","pmids":["34340555"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"TgVAMP4-1 physically interacts with the SM protein TgVps45 and the SNARE protein TgStx16, placing TgVAMP4-1 in a vesicle fusion complex at the trans-Golgi network (TGN) involved in post-Golgi trafficking required for pellicle and sub-pellicle network assembly.","method":"Co-immunoprecipitation (TgVps45 interaction with TgStx16 and TgVAMP4-1), conditional knockout epistasis (TgStx16 ablation phenocopies TgVps45 deficiency)","journal":"Molecular microbiology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP interaction plus genetic epistasis from conditional knockouts; single lab, two complementary methods","pmids":["31670849"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"Toxoplasma gondii encodes two VAMP4 paralogs with distinct localizations and functions: TgVAMP4-1 acts as an R-SNARE at the trans-Golgi network in complex with TgVps45 and TgStx16 to mediate post-Golgi vesicle fusion required for pellicle assembly, while TgVAMP4-2 localizes to the outermost membrane of the apicoplast and is required for vesicular trafficking that imports nucleus-encoded proteins into this secondary endosymbiotic organelle."},"narrative":{"mechanistic_narrative":"In Toxoplasma gondii, VAMP4 is represented by two paralogous R-SNAREs that direct distinct vesicular fusion events supporting organelle biogenesis and protein import [PMID:34340555, PMID:31670849]. TgVAMP4-1 assembles into a trans-Golgi network fusion complex with the SM protein TgVps45 and the syntaxin TgStx16, mediating post-Golgi trafficking required for assembly of the pellicle and sub-pellicle network [PMID:31670849]. TgVAMP4-2 localizes to the outermost membrane of the apicoplast, where it drives the vesicular trafficking that imports nucleus-encoded, apicoplast-targeted proteins (TgCPN60, TgACP, TgATrx2, TgATrx1) into this secondary endosymbiotic organelle and delivers TgAPT1 and TgFtsH1 to its outermost membrane [PMID:34340555]. Beyond these two paralog-specific roles, no further mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2019,"claim":"Whether a VAMP4 paralog participates in post-Golgi membrane fusion in Toxoplasma was unknown; identifying TgVAMP4-1 in a defined TGN fusion complex established its role in trafficking needed for pellicle assembly.","evidence":"Co-immunoprecipitation of TgVps45 with TgStx16 and TgVAMP4-1, plus conditional-knockout epistasis (TgStx16 ablation phenocopies TgVps45 deficiency)","pmids":["31670849"],"confidence":"Medium","gaps":["Direct SNARE-complex assembly and fusion activity not reconstituted","Reciprocal Co-IP validation of the TgVAMP4-1 interaction not reported","Molecular link between the fusion event and specific pellicle/sub-pellicle cargo not defined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2021,"claim":"How nucleus-encoded proteins reach the apicoplast was unresolved; localizing TgVAMP4-2 to the outermost apicoplast membrane and ablating it established an R-SNARE-dependent vesicular import route into this organelle.","evidence":"Conditional knockout with subcellular localization and multiple protein-import readouts (TgCPN60, TgACP, TgATrx2, TgATrx1, TgAPT1, TgFtsH1) in T. gondii","pmids":["34340555"],"confidence":"High","gaps":["Partner SNAREs/tethering factors at the apicoplast membrane not identified","Source compartment of the import vesicles not defined","Mechanism coupling TgVAMP4-2 fusion to cargo translocation across membranes unresolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"It remains unknown how the two paralogs are functionally partitioned and whether they share regulatory or fusion machinery across the TGN and apicoplast compartments.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No shared or paralog-specific interactome comparison reported","No structural model of either SNARE complex","Regulation and directionality of the two trafficking routes uncharacterized"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["TgVAMP4-1–TgVps45–TgStx16 trans-Golgi network SNARE fusion complex"],"partners":["TGVPS45 (SM PROTEIN)","TGSTX16 (SYNTAXIN/SNARE)"],"other_free_text":["Two paralogs with divergent localization and function: TgVAMP4-1 at the TGN in post-Golgi trafficking for pellicle/sub-pellicle assembly; TgVAMP4-2 at the outermost apicoplast membrane for import of nucleus-encoded apicoplast proteins","TgVAMP4-2 import cargo includes TgCPN60, TgACP, TgATrx2, TgATrx1; targeting of TgAPT1 and TgFtsH1 to the outermost apicoplast membrane also depends on TgVAMP4-2"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"34340555","id":"PMC_34340555","title":"The Dissection of SNAREs Reveals Key Factors for Vesicular Trafficking to the Endosome-like Compartment and Apicoplast via the Secretory System in Toxoplasma gondii.","date":"2021","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/34340555","citation_count":20,"is_preprint":false},{"pmid":"31670849","id":"PMC_31670849","title":"The Sec1/Munc18-like proteins TgSec1 and TgVps45 play pivotal roles in assembly of the pellicle and sub-pellicle network in Toxoplasma gondii.","date":"2019","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/31670849","citation_count":12,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3675,"output_tokens":740,"usd":0.011062,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5493,"output_tokens":1999,"usd":0.03872,"stage2_stop_reason":"end_turn"},"total_usd":0.049782,"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\": 2021,\n      \"finding\": \"TgVAMP4-2 is an R-SNARE localized to the outermost membrane of the apicoplast in Toxoplasma gondii, and its conditional knockout blocked import of nucleus-encoded apicoplast-targeted proteins (TgCPN60, TgACP, TgATrx2, TgATrx1) into the apicoplast and interfered with targeting of TgAPT1 and TgFtsH1 to the outermost apicoplast membrane, establishing that TgVAMP4-2 functions in vesicular trafficking required for protein import into this secondary endosymbiotic organelle.\",\n      \"method\": \"Conditional knockout (conditional ablation), subcellular localization analysis, protein import assay\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional knockout with multiple specific protein import readouts, direct localization determination, single lab but multiple orthogonal functional assays\",\n      \"pmids\": [\"34340555\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TgVAMP4-1 physically interacts with the SM protein TgVps45 and the SNARE protein TgStx16, placing TgVAMP4-1 in a vesicle fusion complex at the trans-Golgi network (TGN) involved in post-Golgi trafficking required for pellicle and sub-pellicle network assembly.\",\n      \"method\": \"Co-immunoprecipitation (TgVps45 interaction with TgStx16 and TgVAMP4-1), conditional knockout epistasis (TgStx16 ablation phenocopies TgVps45 deficiency)\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP interaction plus genetic epistasis from conditional knockouts; single lab, two complementary methods\",\n      \"pmids\": [\"31670849\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"Toxoplasma gondii encodes two VAMP4 paralogs with distinct localizations and functions: TgVAMP4-1 acts as an R-SNARE at the trans-Golgi network in complex with TgVps45 and TgStx16 to mediate post-Golgi vesicle fusion required for pellicle assembly, while TgVAMP4-2 localizes to the outermost membrane of the apicoplast and is required for vesicular trafficking that imports nucleus-encoded proteins into this secondary endosymbiotic organelle.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"In Toxoplasma gondii, VAMP4 is represented by two paralogous R-SNAREs that direct distinct vesicular fusion events supporting organelle biogenesis and protein import [#0, #1]. TgVAMP4-1 assembles into a trans-Golgi network fusion complex with the SM protein TgVps45 and the syntaxin TgStx16, mediating post-Golgi trafficking required for assembly of the pellicle and sub-pellicle network [#1]. TgVAMP4-2 localizes to the outermost membrane of the apicoplast, where it drives the vesicular trafficking that imports nucleus-encoded, apicoplast-targeted proteins (TgCPN60, TgACP, TgATrx2, TgATrx1) into this secondary endosymbiotic organelle and delivers TgAPT1 and TgFtsH1 to its outermost membrane [#0]. Beyond these two paralog-specific roles, no further mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Whether a VAMP4 paralog participates in post-Golgi membrane fusion in Toxoplasma was unknown; identifying TgVAMP4-1 in a defined TGN fusion complex established its role in trafficking needed for pellicle assembly.\",\n      \"evidence\": \"Co-immunoprecipitation of TgVps45 with TgStx16 and TgVAMP4-1, plus conditional-knockout epistasis (TgStx16 ablation phenocopies TgVps45 deficiency)\",\n      \"pmids\": [\"31670849\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct SNARE-complex assembly and fusion activity not reconstituted\",\n        \"Reciprocal Co-IP validation of the TgVAMP4-1 interaction not reported\",\n        \"Molecular link between the fusion event and specific pellicle/sub-pellicle cargo not defined\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"How nucleus-encoded proteins reach the apicoplast was unresolved; localizing TgVAMP4-2 to the outermost apicoplast membrane and ablating it established an R-SNARE-dependent vesicular import route into this organelle.\",\n      \"evidence\": \"Conditional knockout with subcellular localization and multiple protein-import readouts (TgCPN60, TgACP, TgATrx2, TgATrx1, TgAPT1, TgFtsH1) in T. gondii\",\n      \"pmids\": [\"34340555\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Partner SNAREs/tethering factors at the apicoplast membrane not identified\",\n        \"Source compartment of the import vesicles not defined\",\n        \"Mechanism coupling TgVAMP4-2 fusion to cargo translocation across membranes unresolved\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how the two paralogs are functionally partitioned and whether they share regulatory or fusion machinery across the TGN and apicoplast compartments.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No shared or paralog-specific interactome comparison reported\",\n        \"No structural model of either SNARE complex\",\n        \"Regulation and directionality of the two trafficking routes uncharacterized\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005484\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005802\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0009507\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006886\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0006906\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\n      \"TgVAMP4-1–TgVps45–TgStx16 trans-Golgi network SNARE fusion complex\"\n    ],\n    \"partners\": [\n      \"TgVps45 (SM protein)\",\n      \"TgStx16 (syntaxin/SNARE)\"\n    ],\n    \"other_free_text\": [\n      \"Two paralogs with divergent localization and function: TgVAMP4-1 at the TGN in post-Golgi trafficking for pellicle/sub-pellicle assembly; TgVAMP4-2 at the outermost apicoplast membrane for import of nucleus-encoded apicoplast proteins\",\n      \"TgVAMP4-2 import cargo includes TgCPN60, TgACP, TgATrx2, TgATrx1; targeting of TgAPT1 and TgFtsH1 to the outermost apicoplast membrane also depends on TgVAMP4-2\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_246610","name":null,"product":"vesicle-associated membrane protein VAMP4","uniprot_acc":"S8G050","chromosome":"TGME49_chrXII","start_pos":2882173},{"strain":"GT1","gene_id":"TGGT1_246610","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrXII","start_pos":2815347},{"strain":"RH88","gene_id":"TGRH88_060880","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023093","start_pos":2913784},{"strain":"VEG","gene_id":"TGVEG_246610","name":null,"product":"synaptobrevin","uniprot_acc":"A0A125YJW5","chromosome":"TGVEG_chrXII","start_pos":2852898}]}