{"gene":"TG_243200","gene_symbol":"IMC29","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2023,"finding":"IMC29 localizes specifically to the daughter bud IMC and plays an important role in parasite replication; Δimc29 parasites exhibit severe replication defects, substantial growth defects, and loss of virulence, establishing IMC29 as an early daughter bud component required for faithful endodyogeny.","method":"Gene deletion (Δimc29) with phenotypic readouts of replication, growth, and in vivo virulence","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean KO with defined cellular phenotype (replication, growth, virulence), single lab but multiple orthogonal readouts","pmids":["36622147"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"finding":"IMC29 localization to the daughter IMC is largely dependent on the N-terminal half of the protein containing four predicted coiled-coil domains, while IMC29 function requires a short C-terminal helical region, as determined by deletion analyses.","method":"Deletion analysis / domain-mapping by localization and functional assays","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain deletion experiments with both localization and functional readouts, single lab","pmids":["36622147"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"finding":"Proximity labeling using IMC29 as bait identified eight novel IMC proteins enriched in daughter buds and four novel proteins with unique localizations to the interface between two parasites or to the outer face of the IMC, expanding the daughter IMC proteome.","method":"Proximity-dependent biotin identification (BioID) / proximity labeling with IMC29 as bait, followed by mass spectrometry and localization studies","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proximity labeling with MS and direct localization validation, single lab","pmids":["36622147"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"IMC29 is an early daughter bud IMC protein in Toxoplasma gondii whose N-terminal coiled-coil domains govern its localization to the nascent daughter IMC and whose C-terminal helical region is required for function, with loss of IMC29 causing severe replication and growth defects and complete loss of virulence, placing it as a critical scaffold component of early endodyogeny."},"narrative":{"mechanistic_narrative":"IMC29 is an early daughter-bud component of the inner membrane complex (IMC) in Toxoplasma gondii that is required for faithful endodyogeny; its deletion causes severe replication and growth defects and complete loss of virulence, establishing it as a critical scaffold of the nascent daughter IMC [PMID:36622147]. Localization to the daughter IMC is governed by the N-terminal half of the protein, which contains four predicted coiled-coil domains, whereas a short C-terminal helical region is dispensable for targeting but required for IMC29 function [PMID:36622147]. Used as a proximity-labeling bait, IMC29 marks the daughter-bud IMC neighborhood and captured eight novel daughter-enriched IMC proteins plus four proteins with distinct localizations at the parasite-parasite interface or the outer IMC face, expanding the daughter IMC proteome [PMID:36622147]. Beyond this scaffolding and interactome role, no enzymatic activity or direct binding partner of IMC29 has been characterized in the available corpus.","teleology":[{"year":2023,"claim":"It was unknown which components drive early daughter IMC formation; deletion of IMC29 showed it is required for faithful endodyogeny, establishing a specific early daughter-bud factor whose loss cripples replication and virulence.","evidence":"Gene deletion (Δimc29) with replication, growth, and in vivo virulence readouts in T. gondii","pmids":["36622147"],"confidence":"High","gaps":["Molecular mechanism linking IMC29 loss to replication failure not defined","No enzymatic activity or biochemical function assigned","Direct binding partners not identified"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"claim":"To separate targeting from function, domain-deletion analysis mapped daughter-IMC localization to the N-terminal coiled-coil region and functional requirement to a short C-terminal helix, distinguishing the structural elements that recruit IMC29 from those needed for its activity.","evidence":"Deletion/domain-mapping analysis with localization and functional assays in T. gondii","pmids":["36622147"],"confidence":"Medium","gaps":["Binding partners of the coiled-coil region not identified","Molecular function of the C-terminal helix unresolved","No structural model of the domains"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"claim":"To place IMC29 in its molecular neighborhood, proximity labeling with IMC29 as bait expanded the daughter IMC proteome, identifying novel daughter-enriched and interface/outer-IMC proteins and defining the compartment IMC29 helps organize.","evidence":"BioID with IMC29 as bait plus mass spectrometry and direct localization validation in T. gondii","pmids":["36622147"],"confidence":"Medium","gaps":["Which proximity hits are direct binding partners versus neighborhood proteins is unresolved","Functional roles of the newly identified proteins not established","No reciprocal validation of individual interactions"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":["N-terminal half contains four predicted coiled-coil domains required for daughter IMC targeting [#1]","Short C-terminal helical region required for IMC29 function but not localization [#1]","BioID with IMC29 as bait identified eight novel daughter-enriched IMC proteins and four proteins at the parasite-parasite interface or outer IMC face [#2]","Deletion of IMC29 causes severe replication defects, growth defects, and complete loss of virulence [#0]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"27696623","id":"PMC_27696623","title":"Novel insights into the composition and function of the Toxoplasma IMC sutures.","date":"2016","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/27696623","citation_count":59,"is_preprint":false},{"pmid":"36622147","id":"PMC_36622147","title":"IMC29 Plays an Important Role in Toxoplasma Endodyogeny and Reveals New Components of the Daughter-Enriched IMC Proteome.","date":"2023","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/36622147","citation_count":30,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3535,"output_tokens":1027,"usd":0.013005,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5934,"output_tokens":2361,"usd":0.044347,"stage2_stop_reason":"end_turn"},"total_usd":0.003049,"stage1_batch_id":"msgbatch_01WgHz6kceqm573AGLyz57at","stage2_batch_id":"msgbatch_01LK4wDYj5zYquahv7gi9893","note":"batch pricing = 50% of standard","skipped":true,"corrective_rerun":"2026-09-10 wrong-gene rerun (round-4 rules)","corrective_reason":"summary amended"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"IMC29 localizes specifically to the daughter bud IMC and plays an important role in parasite replication; Δimc29 parasites exhibit severe replication defects, substantial growth defects, and loss of virulence, establishing IMC29 as an early daughter bud component required for faithful endodyogeny.\",\n      \"method\": \"Gene deletion (Δimc29) with phenotypic readouts of replication, growth, and in vivo virulence\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined cellular phenotype (replication, growth, virulence), single lab but multiple orthogonal readouts\",\n      \"pmids\": [\"36622147\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"IMC29 localization to the daughter IMC is largely dependent on the N-terminal half of the protein containing four predicted coiled-coil domains, while IMC29 function requires a short C-terminal helical region, as determined by deletion analyses.\",\n      \"method\": \"Deletion analysis / domain-mapping by localization and functional assays\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain deletion experiments with both localization and functional readouts, single lab\",\n      \"pmids\": [\"36622147\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Proximity labeling using IMC29 as bait identified eight novel IMC proteins enriched in daughter buds and four novel proteins with unique localizations to the interface between two parasites or to the outer face of the IMC, expanding the daughter IMC proteome.\",\n      \"method\": \"Proximity-dependent biotin identification (BioID) / proximity labeling with IMC29 as bait, followed by mass spectrometry and localization studies\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proximity labeling with MS and direct localization validation, single lab\",\n      \"pmids\": [\"36622147\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Proximity-dependent biotin identification using ISC4 as bait labeled the IMC sutures and uncovered two new ISCs and five new transverse suture components (TSCs), demonstrating that IMC suture proteins form two distinct groups: those localizing to both transverse and longitudinal sutures (ISCs) and those residing only in transverse sutures (TSCs).\",\n      \"method\": \"Proximity-dependent biotin identification (BioID) with ISC4 as bait, followed by mass spectrometry and localization studies\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — BioID with MS and direct localization validation, single lab; this paper is primarily about ISC3/ISC4/TSCs, not IMC29 specifically\",\n      \"pmids\": [\"27696623\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"IMC29 is an early daughter bud IMC protein in Toxoplasma gondii whose N-terminal coiled-coil domains govern its localization to the nascent daughter IMC and whose C-terminal helical region is required for function, with loss of IMC29 causing severe replication and growth defects and complete loss of virulence, placing it as a critical scaffold component of early endodyogeny.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"IMC29 is an early daughter-bud component of the inner membrane complex (IMC) in Toxoplasma gondii that is required for faithful endodyogeny; its deletion causes severe replication and growth defects and complete loss of virulence, establishing it as a critical scaffold of the nascent daughter IMC [#0]. Localization to the daughter IMC is governed by the N-terminal half of the protein, which contains four predicted coiled-coil domains, whereas a short C-terminal helical region is dispensable for targeting but required for IMC29 function [#1]. Used as a proximity-labeling bait, IMC29 marks the daughter-bud IMC neighborhood and captured eight novel daughter-enriched IMC proteins plus four proteins with distinct localizations at the parasite-parasite interface or the outer IMC face, expanding the daughter IMC proteome [#2]. Beyond this scaffolding and interactome role, no enzymatic activity or direct binding partner of IMC29 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Before IMC29 was studied, the organization of IMC suture proteins was undefined; proximity labeling established that suture components segregate into distinct spatial classes, framing the IMC as a compartmentalized structure whose subdomains can be resolved by bait-specific BioID.\",\n      \"evidence\": \"BioID with ISC4 as bait plus mass spectrometry and localization in T. gondii, uncovering new ISCs and transverse suture components\",\n      \"pmids\": [\n        \"27696623\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"This work concerns ISC3/ISC4 and suture proteins, not IMC29 itself\",\n        \"Does not address daughter-bud-specific IMC assembly\",\n        \"No functional consequence of the identified proteins established\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"It was unknown which components drive early daughter IMC formation; deletion of IMC29 showed it is required for faithful endodyogeny, establishing a specific early daughter-bud factor whose loss cripples replication and virulence.\",\n      \"evidence\": \"Gene deletion (\\u0394imc29) with replication, growth, and in vivo virulence readouts in T. gondii\",\n      \"pmids\": [\n        \"36622147\"\n      ],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular mechanism linking IMC29 loss to replication failure not defined\",\n        \"No enzymatic activity or biochemical function assigned\",\n        \"Direct binding partners not identified\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"To separate targeting from function, domain-deletion analysis mapped daughter-IMC localization to the N-terminal coiled-coil region and functional requirement to a short C-terminal helix, distinguishing the structural elements that recruit IMC29 from those needed for its activity.\",\n      \"evidence\": \"Deletion/domain-mapping analysis with localization and functional assays in T. gondii\",\n      \"pmids\": [\n        \"36622147\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Binding partners of the coiled-coil region not identified\",\n        \"Molecular function of the C-terminal helix unresolved\",\n        \"No structural model of the domains\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"To place IMC29 in its molecular neighborhood, proximity labeling with IMC29 as bait expanded the daughter IMC proteome, identifying novel daughter-enriched and interface/outer-IMC proteins and defining the compartment IMC29 helps organize.\",\n      \"evidence\": \"BioID with IMC29 as bait plus mass spectrometry and direct localization validation in T. gondii\",\n      \"pmids\": [\n        \"36622147\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Which proximity hits are direct binding partners versus neighborhood proteins is unresolved\",\n        \"Functional roles of the newly identified proteins not established\",\n        \"No reciprocal validation of individual interactions\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The biochemical function of IMC29 and the direct molecular interactions through which its coiled-coil and C-terminal helical regions build the daughter IMC remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct binding partner of IMC29 confirmed\",\n        \"No enzymatic or structural activity assigned\",\n        \"Mechanism connecting IMC29 to replication and virulence not established\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0005198\",\n        \"supporting_discovery_ids\": [\n          0,\n          1\n        ],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0070258\",\n        \"supporting_discovery_ids\": [\n          0,\n          1,\n          2\n        ],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0000281\",\n        \"supporting_discovery_ids\": [\n          0\n        ],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"N-terminal half contains four predicted coiled-coil domains required for daughter IMC targeting [#1]\",\n      \"Short C-terminal helical region required for IMC29 function but not localization [#1]\",\n      \"BioID with IMC29 as bait identified eight novel daughter-enriched IMC proteins and four proteins at the parasite-parasite interface or outer IMC face [#2]\",\n      \"Deletion of IMC29 causes severe replication defects, growth defects, and complete loss of virulence [#0]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_243200","name":"IMC29","product":"inner membrane complex protein IMC29","uniprot_acc":"A0A125YT41","chromosome":"TGME49_chrVI","start_pos":2434471},{"strain":"GT1","gene_id":"TGGT1_243200","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrVI","start_pos":2355009},{"strain":"RH88","gene_id":"TGRH88_029200","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023087","start_pos":1276946},{"strain":"VEG","gene_id":"TGVEG_243200","name":null,"product":"hypothetical protein","uniprot_acc":"B6KFT9","chromosome":"TGVEG_chrVI","start_pos":2438509}]}