{"gene":"TG_263290","gene_symbol":"ROM2","run_date":"2026-09-08T14:08:29","timeline":{"discoveries":[{"year":2005,"finding":"TgROM2 is an active rhomboid intramembrane serine protease expressed in the oocyst stage; it cleaves the transmembrane domain of Drosophila Spitz and chimeric proteins containing the TM domains of TgMIC2 and TgMIC12 in a cell-based assay.","method":"Cell-based cleavage assay using established rhomboid substrates (Drosophila Spitz) and chimeric constructs containing TgMIC2/TgMIC12 TM domains","journal":"International journal for parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cell-based functional assay with multiple substrates in a single lab; confirms enzymatic activity but no mutagenesis or structural validation reported in abstract","pmids":["15913633"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2005,"finding":"TgROM2 is expressed in the oocyst stage (not in tachyzoites), in contrast to TgROM1, TgROM4, and TgROM5 which are expressed in tachyzoites.","method":"Gene cloning and expression profiling of T. gondii rhomboid family members across life stages","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — stage-specific expression established by molecular characterization in two independent studies (PMID 15753289 and 15913633)","pmids":["15753289","15913633"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2008,"finding":"TgROM2 localizes to the Golgi apparatus, and its N-terminal cytosolic domain contains critical sorting determinants responsible for this Golgi localization, as established by domain-exchange and site-directed mutagenesis experiments.","method":"Subcellular fractionation/localization, domain-exchange experiments, site-directed mutagenesis of N-terminal cytosolic domain","journal":"Traffic (Copenhagen, Denmark)","confidence":"High","confidence_rationale":"Tier 2 / Moderate — direct localization experiment combined with domain-swap and mutagenesis to map functional sorting determinants, single lab but multiple orthogonal methods","pmids":["18346213"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"TgROM2 is a Golgi-localized active rhomboid intramembrane serine protease expressed in the oocyst stage of Toxoplasma gondii, capable of cleaving microneme protein transmembrane domains (TgMIC2, TgMIC12) in cell-based assays, with its Golgi targeting determined by critical sorting determinants in its N-terminal cytosolic domain."},"narrative":{"mechanistic_narrative":"TgROM2 is an active rhomboid intramembrane serine protease of Toxoplasma gondii whose expression is restricted to the oocyst stage, distinguishing it from the tachyzoite-expressed rhomboids TgROM1, TgROM4, and TgROM5 [PMID:15913633, PMID:15753289]. In cell-based cleavage assays it processes the transmembrane domain of the canonical rhomboid substrate Drosophila Spitz as well as chimeric proteins bearing the transmembrane domains of the microneme proteins TgMIC2 and TgMIC12, establishing its capacity to cleave micronemal TM segments [PMID:15913633]. The enzyme localizes to the Golgi apparatus, and this targeting is directed by critical sorting determinants residing in its N-terminal cytosolic domain, as mapped by domain-exchange and site-directed mutagenesis [PMID:18346213]. Beyond these findings, the physiological substrates, in vivo function during the oocyst stage, and structural basis of catalysis have not been characterized in the available corpus.","teleology":[{"year":2005,"claim":"Whether TgROM2 is a functional protease and what class of substrates it can act on was unknown; demonstrating cleavage of rhomboid substrates established it as a catalytically active intramembrane serine protease with specificity for microneme protein TM domains.","evidence":"Cell-based cleavage assay with Drosophila Spitz and chimeric TgMIC2/TgMIC12 TM-domain constructs in T. gondii","pmids":["15913633"],"confidence":"Medium","gaps":["No mutagenesis of the catalytic serine to confirm the active-site mechanism","Native full-length microneme substrates not tested, only chimeric TM constructs","No structural validation of substrate recognition"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2005,"claim":"The life-cycle stage in which TgROM2 operates was undefined; expression profiling placed it exclusively in the oocyst stage, separating its biological role from the tachyzoite rhomboids TgROM1/4/5.","evidence":"Gene cloning and stage-specific expression profiling of the T. gondii rhomboid family","pmids":["15753289","15913633"],"confidence":"Medium","gaps":["Functional role within the oocyst stage not established","No genetic knockout to test requirement in vivo"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2008,"claim":"Where TgROM2 acts within the cell and how it is targeted there was unknown; localization combined with domain-swap and mutagenesis showed Golgi residence dictated by sorting determinants in the N-terminal cytosolic domain.","evidence":"Subcellular localization, domain-exchange, and site-directed mutagenesis in T. gondii","pmids":["18346213"],"confidence":"High","gaps":["Identity of the trafficking machinery recognizing the N-terminal determinants not defined","Whether Golgi localization is required for physiological substrate processing not tested"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"The endogenous physiological substrates of TgROM2 and its functional requirement during the oocyst stage remain undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No in vivo substrate identified","No loss-of-function phenotype established","No structural model of the enzyme"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":["Oocyst-stage-specific expression, unlike the tachyzoite rhomboids TgROM1, TgROM4, TgROM5 [#1]","Cleaves TM domains of Drosophila Spitz and chimeric TgMIC2/TgMIC12 constructs in cell-based assays [#0]","Golgi targeting mediated by sorting determinants in the N-terminal cytosolic domain [#2]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"15753289","id":"PMC_15753289","title":"A spatially localized rhomboid protease cleaves cell surface adhesins essential for invasion by Toxoplasma.","date":"2005","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/15753289","citation_count":171,"is_preprint":false},{"pmid":"15913633","id":"PMC_15913633","title":"Apicomplexan rhomboids have a potential role in microneme protein cleavage during host cell invasion.","date":"2005","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/15913633","citation_count":98,"is_preprint":false},{"pmid":"15358257","id":"PMC_15358257","title":"Host cell invasion by the apicomplexans: the significance of microneme protein proteolysis.","date":"2004","source":"Current opinion in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/15358257","citation_count":72,"is_preprint":false},{"pmid":"18346213","id":"PMC_18346213","title":"Identification of trafficking determinants for polytopic rhomboid proteases in Toxoplasma gondii.","date":"2008","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/18346213","citation_count":27,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4032,"output_tokens":856,"usd":0.012468,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5651,"output_tokens":1726,"usd":0.035702,"stage2_stop_reason":"end_turn"},"total_usd":0.04817,"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\": 2005,\n      \"finding\": \"TgROM2 is an active rhomboid intramembrane serine protease expressed in the oocyst stage; it cleaves the transmembrane domain of Drosophila Spitz and chimeric proteins containing the TM domains of TgMIC2 and TgMIC12 in a cell-based assay.\",\n      \"method\": \"Cell-based cleavage assay using established rhomboid substrates (Drosophila Spitz) and chimeric constructs containing TgMIC2/TgMIC12 TM domains\",\n      \"journal\": \"International journal for parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-based functional assay with multiple substrates in a single lab; confirms enzymatic activity but no mutagenesis or structural validation reported in abstract\",\n      \"pmids\": [\"15913633\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"TgROM2 is expressed in the oocyst stage (not in tachyzoites), in contrast to TgROM1, TgROM4, and TgROM5 which are expressed in tachyzoites.\",\n      \"method\": \"Gene cloning and expression profiling of T. gondii rhomboid family members across life stages\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — stage-specific expression established by molecular characterization in two independent studies (PMID 15753289 and 15913633)\",\n      \"pmids\": [\"15753289\", \"15913633\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"TgROM2 localizes to the Golgi apparatus, and its N-terminal cytosolic domain contains critical sorting determinants responsible for this Golgi localization, as established by domain-exchange and site-directed mutagenesis experiments.\",\n      \"method\": \"Subcellular fractionation/localization, domain-exchange experiments, site-directed mutagenesis of N-terminal cytosolic domain\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment combined with domain-swap and mutagenesis to map functional sorting determinants, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"18346213\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"TgROM2 is a Golgi-localized active rhomboid intramembrane serine protease expressed in the oocyst stage of Toxoplasma gondii, capable of cleaving microneme protein transmembrane domains (TgMIC2, TgMIC12) in cell-based assays, with its Golgi targeting determined by critical sorting determinants in its N-terminal cytosolic domain.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TgROM2 is an active rhomboid intramembrane serine protease of Toxoplasma gondii whose expression is restricted to the oocyst stage, distinguishing it from the tachyzoite-expressed rhomboids TgROM1, TgROM4, and TgROM5 [#0, #1]. In cell-based cleavage assays it processes the transmembrane domain of the canonical rhomboid substrate Drosophila Spitz as well as chimeric proteins bearing the transmembrane domains of the microneme proteins TgMIC2 and TgMIC12, establishing its capacity to cleave micronemal TM segments [#0]. The enzyme localizes to the Golgi apparatus, and this targeting is directed by critical sorting determinants residing in its N-terminal cytosolic domain, as mapped by domain-exchange and site-directed mutagenesis [#2]. Beyond these findings, the physiological substrates, in vivo function during the oocyst stage, and structural basis of catalysis have not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Whether TgROM2 is a functional protease and what class of substrates it can act on was unknown; demonstrating cleavage of rhomboid substrates established it as a catalytically active intramembrane serine protease with specificity for microneme protein TM domains.\",\n      \"evidence\": \"Cell-based cleavage assay with Drosophila Spitz and chimeric TgMIC2/TgMIC12 TM-domain constructs in T. gondii\",\n      \"pmids\": [\"15913633\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No mutagenesis of the catalytic serine to confirm the active-site mechanism\", \"Native full-length microneme substrates not tested, only chimeric TM constructs\", \"No structural validation of substrate recognition\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"The life-cycle stage in which TgROM2 operates was undefined; expression profiling placed it exclusively in the oocyst stage, separating its biological role from the tachyzoite rhomboids TgROM1/4/5.\",\n      \"evidence\": \"Gene cloning and stage-specific expression profiling of the T. gondii rhomboid family\",\n      \"pmids\": [\"15753289\", \"15913633\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional role within the oocyst stage not established\", \"No genetic knockout to test requirement in vivo\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Where TgROM2 acts within the cell and how it is targeted there was unknown; localization combined with domain-swap and mutagenesis showed Golgi residence dictated by sorting determinants in the N-terminal cytosolic domain.\",\n      \"evidence\": \"Subcellular localization, domain-exchange, and site-directed mutagenesis in T. gondii\",\n      \"pmids\": [\"18346213\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the trafficking machinery recognizing the N-terminal determinants not defined\", \"Whether Golgi localization is required for physiological substrate processing not tested\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The endogenous physiological substrates of TgROM2 and its functional requirement during the oocyst stage remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vivo substrate identified\", \"No loss-of-function phenotype established\", \"No structural model of the enzyme\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004252\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Oocyst-stage-specific expression, unlike the tachyzoite rhomboids TgROM1, TgROM4, TgROM5 [#1]\",\n      \"Cleaves TM domains of Drosophila Spitz and chimeric TgMIC2/TgMIC12 constructs in cell-based assays [#0]\",\n      \"Golgi targeting mediated by sorting determinants in the N-terminal cytosolic domain [#2]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_263290","name":"ROM2","product":"rhomboid protease ROM2","uniprot_acc":"S8GD47","chromosome":"TGME49_chrVIIb","start_pos":650740},{"strain":"GT1","gene_id":"TGGT1_263290","name":null,"product":"rhomboid protease ROM2","uniprot_acc":null,"chromosome":"TGGT1_chrVIIb","start_pos":625248},{"strain":"RH88","gene_id":"TGRH88_067720","name":null,"product":"rhomboid protease ROM2","uniprot_acc":null,"chromosome":"CM023089","start_pos":663502},{"strain":"VEG","gene_id":"TGVEG_263290","name":null,"product":"rhomboid protease ROM2","uniprot_acc":"B9QNZ0","chromosome":"TGVEG_chrVIIb","start_pos":656347}]}