{"gene":"TG_229020","gene_symbol":"CRK5","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2017,"finding":"TgCrk5 forms a stable complex with ECR1 (Essential for Chromosome Replication 1), a 52-kDa protein containing divergent RING and TRAF-Sina-like zinc binding domains. Both TgCrk5 and ECR1 display similar cell cycle expression patterns and co-localize in the centrocone (the apicomplexan-specific spindle compartment of the nuclear envelope) during tachyzoite replication, indicating TgCrk5 is part of a regulatory mechanism controlling chromosome replication and mitotic processes.","method":"Co-immunoprecipitation/proteomics, immunofluorescence microscopy, cell cycle expression analysis","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP/proteomics plus colocalization by immunofluorescence, single lab, two orthogonal methods","pmids":["28830940"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"finding":"TgCrk5 localizes to the centrocone (the apicomplexan-specific spindle compartment) of the nuclear envelope during early S phase, with a dynamic cell cycle-regulated expression pattern in tachyzoites, placing it spatially at a key site of cell cycle regulation.","method":"Immunofluorescence microscopy, cell cycle staging","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by immunofluorescence with cell cycle staging, single lab, two methods (localization + expression dynamics)","pmids":["28830940"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"TgCrk5 is a CDK-related kinase that localizes to the apicomplexan-specific centrocone spindle compartment during tachyzoite replication, where it forms a stable complex with ECR1 (a putative E3 ligase involved in regulating chromosome replication and mitotic processes), suggesting TgCrk5 participates in cell cycle regulation at the centrocone, though its precise substrates and essentiality remain uncharacterized."},"narrative":{"mechanistic_narrative":"TgCrk5 is a CDK-related kinase implicated in the regulation of chromosome replication and mitotic progression in Toxoplasma gondii tachyzoites [PMID:28830940]. It localizes to the centrocone, the apicomplexan-specific spindle compartment of the nuclear envelope, during early S phase and displays a dynamic, cell cycle-regulated expression pattern that places it spatially at a key site of cell cycle control [PMID:28830940]. At this location it forms a stable complex with ECR1, a 52-kDa protein bearing divergent RING and TRAF-Sina-like zinc-binding domains, with which it shares cell cycle expression dynamics and co-localization [PMID:28830940].","teleology":[{"year":2017,"claim":"Establishing where in the cell cycle machinery TgCrk5 acts, immunofluorescence placed it at the centrocone during early S phase, identifying it as a candidate regulator situated at the apicomplexan mitotic spindle compartment.","evidence":"Immunofluorescence microscopy with cell cycle staging in tachyzoites","pmids":["28830940"],"confidence":"Medium","gaps":["Kinase activity and substrates at the centrocone not identified","Functional consequence of centrocone localization untested","Mechanism of recruitment to the centrocone unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"claim":"To identify TgCrk5's regulatory partners, co-IP/proteomics and colocalization revealed a stable complex with ECR1, linking the kinase to a putative E3 ligase and a mechanism controlling chromosome replication and mitosis.","evidence":"Co-immunoprecipitation/proteomics, immunofluorescence colocalization, and cell cycle expression analysis in T. gondii","pmids":["28830940"],"confidence":"Medium","gaps":["ECR1 E3 ligase activity and its relationship to TgCrk5 phosphorylation not demonstrated","No reciprocal validation of the interaction reported","Whether TgCrk5 phosphorylates ECR1 or vice versa unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["TgCrk5-ECR1 complex"],"partners":["ECR1 (ESSENTIAL FOR CHROMOSOME REPLICATION 1)"],"other_free_text":["Localizes to the centrocone during early S phase with cell cycle-regulated expression.","Not reported essential for tachyzoite growth and did not interact with any tested cyclin, suggesting cyclin-independent function."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"10873834","id":"PMC_10873834","title":"Intracellular targets of cyclin-dependent kinase inhibitors: identification by affinity chromatography using immobilised inhibitors.","date":"2000","source":"Chemistry & biology","url":"https://pubmed.ncbi.nlm.nih.gov/10873834","citation_count":202,"is_preprint":false},{"pmid":"15023358","id":"PMC_15023358","title":"Protein kinases as targets for anti-parasitic chemotherapy.","date":"2004","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/15023358","citation_count":113,"is_preprint":false},{"pmid":"18703066","id":"PMC_18703066","title":"The cell cycle and Toxoplasma gondii cell division: tightly knit or loosely stitched?","date":"2008","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/18703066","citation_count":82,"is_preprint":false},{"pmid":"28830940","id":"PMC_28830940","title":"The Toxoplasma Centrocone Houses Cell Cycle Regulatory Factors.","date":"2017","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/28830940","citation_count":26,"is_preprint":false},{"pmid":"15811523","id":"PMC_15811523","title":"Characterization of two T. gondii CK1 isoforms.","date":"2005","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/15811523","citation_count":26,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9774,"output_tokens":904,"usd":0.021441,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5723,"output_tokens":1972,"usd":0.038957,"stage2_stop_reason":"end_turn"},"total_usd":0.060398,"stage1_batch_id":"msgbatch_01WokvBYTB6JLnYrpD4rXnyV","stage2_batch_id":"msgbatch_01M7hsQDvz6AqVC9DLVjQzzc","note":"batch pricing = 50% of standard","corrective_rerun":"2026-09-10 wrong-gene rerun (round-4 rules)","corrective_reason":"summary amended"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"TgCrk5 forms a stable complex with ECR1 (Essential for Chromosome Replication 1), a 52-kDa protein containing divergent RING and TRAF-Sina-like zinc binding domains. Both TgCrk5 and ECR1 display similar cell cycle expression patterns and co-localize in the centrocone (the apicomplexan-specific spindle compartment of the nuclear envelope) during tachyzoite replication, indicating TgCrk5 is part of a regulatory mechanism controlling chromosome replication and mitotic processes.\",\n      \"method\": \"Co-immunoprecipitation/proteomics, immunofluorescence microscopy, cell cycle expression analysis\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP/proteomics plus colocalization by immunofluorescence, single lab, two orthogonal methods\",\n      \"pmids\": [\"28830940\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TgCrk5 localizes to the centrocone (the apicomplexan-specific spindle compartment) of the nuclear envelope during early S phase, with a dynamic cell cycle-regulated expression pattern in tachyzoites, placing it spatially at a key site of cell cycle regulation.\",\n      \"method\": \"Immunofluorescence microscopy, cell cycle staging\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by immunofluorescence with cell cycle staging, single lab, two methods (localization + expression dynamics)\",\n      \"pmids\": [\"28830940\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Among the seven TgCrks analyzed by conditional tet-OFF mutants, TgCrk5 was not reported as essential for tachyzoite growth (unlike TgCrk1, TgCrk2, TgCrk4, and TgCrk6), and did not interact with any tested cyclin in the study, suggesting it may function independently of a canonical cyclin partner.\",\n      \"method\": \"Conditional tet-OFF mutant analysis, co-immunoprecipitation\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — absence of interaction or growth phenotype from single-lab conditional mutant screen; negative result inferred from omission in the paper\",\n      \"pmids\": [\"28671988\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"TgCrk5 is a CDK-related kinase that localizes to the apicomplexan-specific centrocone spindle compartment during tachyzoite replication, where it forms a stable complex with ECR1 (a putative E3 ligase involved in regulating chromosome replication and mitotic processes), suggesting TgCrk5 participates in cell cycle regulation at the centrocone, though its precise substrates and essentiality remain uncharacterized.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TgCrk5 is a CDK-related kinase implicated in the regulation of chromosome replication and mitotic progression in Toxoplasma gondii tachyzoites [#0]. It localizes to the centrocone, the apicomplexan-specific spindle compartment of the nuclear envelope, during early S phase and displays a dynamic, cell cycle-regulated expression pattern that places it spatially at a key site of cell cycle control [#1]. At this location it forms a stable complex with ECR1, a 52-kDa protein bearing divergent RING and TRAF-Sina-like zinc-binding domains, with which it shares cell cycle expression dynamics and co-localization [#0]. Its kinase substrates, catalytic activity, and essentiality have not been characterized in the available corpus, and no canonical cyclin partner was identified [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Establishing where in the cell cycle machinery TgCrk5 acts, immunofluorescence placed it at the centrocone during early S phase, identifying it as a candidate regulator situated at the apicomplexan mitotic spindle compartment.\",\n      \"evidence\": \"Immunofluorescence microscopy with cell cycle staging in tachyzoites\",\n      \"pmids\": [\"28830940\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Kinase activity and substrates at the centrocone not identified\",\n        \"Functional consequence of centrocone localization untested\",\n        \"Mechanism of recruitment to the centrocone unknown\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"To identify TgCrk5's regulatory partners, co-IP/proteomics and colocalization revealed a stable complex with ECR1, linking the kinase to a putative E3 ligase and a mechanism controlling chromosome replication and mitosis.\",\n      \"evidence\": \"Co-immunoprecipitation/proteomics, immunofluorescence colocalization, and cell cycle expression analysis in T. gondii\",\n      \"pmids\": [\"28830940\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"ECR1 E3 ligase activity and its relationship to TgCrk5 phosphorylation not demonstrated\",\n        \"No reciprocal validation of the interaction reported\",\n        \"Whether TgCrk5 phosphorylates ECR1 or vice versa unknown\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"A conditional tet-OFF screen across seven TgCrks addressed whether TgCrk5 is required for growth and cyclin-associated, finding it was not reported essential and interacted with no tested cyclin, hinting at a cyclin-independent mode of action.\",\n      \"evidence\": \"Conditional tet-OFF mutant analysis and co-immunoprecipitation in tachyzoites\",\n      \"pmids\": [\"28671988\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Non-essentiality inferred from omission rather than a directly reported phenotype\",\n        \"Negative cyclin interaction limited to the cyclins tested\",\n        \"Activating partner (if any) for the kinase unidentified\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The catalytic substrates of TgCrk5, its precise contribution to chromosome replication and mitosis, and the functional significance of the TgCrk5-ECR1 complex remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No phosphorylation substrate identified\",\n        \"No structural or biochemical characterization of kinase activity\",\n        \"Functional role of the ECR1 partnership untested by loss-of-function\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004672\", \"supporting_discovery_ids\": [0, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0000922\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0005635\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0051726\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0006260\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\n      \"TgCrk5-ECR1 complex\"\n    ],\n    \"partners\": [\n      \"ECR1 (Essential for Chromosome Replication 1)\"\n    ],\n    \"other_free_text\": [\n      \"Localizes to the centrocone during early S phase with cell cycle-regulated expression.\",\n      \"Not reported essential for tachyzoite growth and did not interact with any tested cyclin, suggesting cyclin-independent function.\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_229020","name":"CRK5","product":"CDK-related protein kinase CRK5","uniprot_acc":"S8GBC4","chromosome":"TGME49_chrVIII","start_pos":26997},{"strain":"GT1","gene_id":"TGGT1_229020","name":null,"product":"putative cell-cycle-associated protein kinase CDK","uniprot_acc":null,"chromosome":"TGGT1_chrVIII","start_pos":25541},{"strain":"RH88","gene_id":"TGRH88_073850","name":null,"product":"putative cell-cycle-associated protein kinase CDK","uniprot_acc":null,"chromosome":"CM023089","start_pos":5136938},{"strain":"VEG","gene_id":"TGVEG_229020","name":null,"product":"putative cell-cycle-associated protein kinase CDK","uniprot_acc":"A0A125YFN7","chromosome":"TGVEG_chrVIII","start_pos":30390}]}