{"gene":"TG_304970","gene_symbol":"CRK1","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2017,"finding":"TgCrk1 and its partner TgCycL are essential for daughter bud assembly in T. gondii tachyzoites; conditional tet-OFF knockdown of TgCrk1 caused failure of daughter bud formation, establishing TgCrk1 as a mitotic kinase required for cytokinesis.","method":"Conditional tet-OFF knockdown with quantitative fluorescence microscopy; co-immunoprecipitation to identify TgCycL as the cyclin partner","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Moderate — conditional genetic knockdown with defined cellular phenotype plus Co-IP identifying cyclin partner, single lab but two orthogonal methods","pmids":["28671988"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"finding":"TgCrk1 interacts with the atypical cyclin TgCycL, forming a complex required for daughter bud assembly during tachyzoite mitosis.","method":"Co-immunoprecipitation","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP with supporting genetic loss-of-function phenotype, single lab","pmids":["28671988"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"finding":"Phosphorylation of TgCrk1 is altered in parasites depleted of the plant-like phosphatase PPKL, placing TgCrk1 downstream of PPKL in a signaling pathway that regulates daughter parasite development; global phosphoproteomics identified this change, and PPKL depletion phenocopies defects consistent with disrupted Crk1-dependent signaling.","method":"Conditional knockdown of PPKL, global phosphoproteomics, Co-immunoprecipitation and proximity labeling","journal":"bioRxiv : the preprint server for biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — phosphoproteomics identified altered Crk1 phosphorylation but direct mechanistic link (writer/eraser identity, specific sites, functional rescue) not established; preprint single lab","pmids":["37398039"],"is_preprint":true,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"finding":"Phosphorylation of TgCrk1 is altered in PPKL-depleted parasites, suggesting PPKL regulates the Crk1-dependent signaling pathway controlling daughter cell assembly; this was corroborated in the peer-reviewed publication of the same work.","method":"Conditional knockdown of PPKL with global phosphoproteomics","journal":"mBio","confidence":"Low","confidence_rationale":"Tier 3 / Weak — phosphoproteomics association, no direct biochemical reconstitution of PPKL acting on Crk1, single lab","pmids":["37877735"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"TgCrk1 is a CDK-related kinase that forms a complex with the atypical cyclin TgCycL and is essential for daughter bud assembly during T. gondii tachyzoite endodyogeny; its activity is further regulated post-translationally, as its phosphorylation state is altered by the upstream plant-like phosphatase PPKL, placing TgCrk1 in a PPKL-dependent signaling pathway controlling daughter parasite development."},"narrative":{"mechanistic_narrative":"TgCrk1 is a CDK-related kinase that drives daughter bud assembly during Toxoplasma gondii tachyzoite endodyogeny [PMID:28671988]. It functions in complex with the atypical cyclin TgCycL, and conditional depletion of TgCrk1 blocks daughter bud formation, establishing it as a mitotic kinase essential for cytokinesis [PMID:28671988]. TgCrk1 is embedded in a phosphatase-dependent regulatory pathway: its phosphorylation state is altered upon depletion of the plant-like phosphatase PPKL, placing TgCrk1 downstream of PPKL in signaling that controls daughter parasite development [PMID:37877735]. Beyond this cyclin partnership and PPKL-dependent regulation, the substrates, specific phosphosites, and structural basis of TgCrk1 activity have not been characterized in the available corpus.","teleology":[{"year":2017,"claim":"Whether a CDK-related kinase governs the assembly of daughter parasites was unknown; identifying TgCrk1 as essential for bud formation established it as a mitotic kinase controlling tachyzoite cytokinesis.","evidence":"Conditional tet-OFF knockdown with quantitative fluorescence microscopy in T. gondii tachyzoites","pmids":["28671988"],"confidence":"High","gaps":["Direct kinase substrates driving bud assembly not identified","No structural or catalytic characterization","Activation mechanism of the kinase unresolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"claim":"The cyclin partner conferring specificity was unknown; Co-IP identified the atypical cyclin TgCycL as the binding partner, defining the functional TgCrk1-TgCycL complex.","evidence":"Co-immunoprecipitation with supporting genetic loss-of-function phenotype in T. gondii","pmids":["28671988"],"confidence":"Medium","gaps":["Single Co-IP without reciprocal biochemical reconstitution","Whether TgCycL activates TgCrk1 kinase activity not shown directly","Stoichiometry and additional complex members unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"claim":"Whether TgCrk1 activity is regulated by upstream signaling was unknown; phosphoproteomics upon PPKL depletion showed altered TgCrk1 phosphorylation, placing the kinase in a PPKL-dependent pathway controlling daughter cell assembly.","evidence":"Conditional knockdown of PPKL with global phosphoproteomics, Co-IP and proximity labeling in T. gondii (initially bioRxiv preprint, corroborated in mBio)","pmids":["37398039","37877735"],"confidence":"Low","gaps":["No direct biochemical reconstitution of PPKL acting on TgCrk1","Specific phosphosites and writer/eraser identity not established","Functional rescue of TgCrk1 phosphostate not tested"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"The direct substrates of TgCrk1, the phosphosites governing its activity, and the biochemical mechanism linking PPKL dephosphorylation to TgCrk1 function during endodyogeny remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No TgCrk1 substrate identified","No direct enzyme-substrate reconstitution of the PPKL-TgCrk1 relationship","No structural model of the TgCrk1-TgCycL complex"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["TgCrk1-TgCycL kinase-cyclin complex"],"partners":["TGCYCL (ATYPICAL CYCLIN)","PPKL (PLANT-LIKE PHOSPHATASE, UPSTREAM REGULATOR)"],"other_free_text":["TgCrk1 is a CDK-related kinase essential for daughter bud assembly during tachyzoite endodyogeny.","TgCrk1 phosphorylation state is altered upon PPKL depletion, placing it downstream of PPKL signaling."]},"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":"28671988","id":"PMC_28671988","title":"Checkpoints of apicomplexan cell division identified in Toxoplasma gondii.","date":"2017","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/28671988","citation_count":59,"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},{"pmid":"37877735","id":"PMC_37877735","title":"The protein phosphatase PPKL is a key regulator of daughter parasite development in Toxoplasma gondii.","date":"2023","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/37877735","citation_count":15,"is_preprint":false},{"pmid":"37398039","id":"PMC_37398039","title":"The protein phosphatase PPKL is a key regulator of daughter parasite development in Toxoplasma gondii.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37398039","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10632,"output_tokens":1072,"usd":0.023988,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5977,"output_tokens":1932,"usd":0.039093,"stage2_stop_reason":"end_turn"},"total_usd":0.063081,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","note":"batch pricing = 50% of standard","corrective_rerun":"2026-09-10 wrong-gene rerun (round-4 rules)","corrective_reason":"paper list: removed papers about other genes"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"TgCrk1 and its partner TgCycL are essential for daughter bud assembly in T. gondii tachyzoites; conditional tet-OFF knockdown of TgCrk1 caused failure of daughter bud formation, establishing TgCrk1 as a mitotic kinase required for cytokinesis.\",\n      \"method\": \"Conditional tet-OFF knockdown with quantitative fluorescence microscopy; co-immunoprecipitation to identify TgCycL as the cyclin partner\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional genetic knockdown with defined cellular phenotype plus Co-IP identifying cyclin partner, single lab but two orthogonal methods\",\n      \"pmids\": [\"28671988\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TgCrk1 interacts with the atypical cyclin TgCycL, forming a complex required for daughter bud assembly during tachyzoite mitosis.\",\n      \"method\": \"Co-immunoprecipitation\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP with supporting genetic loss-of-function phenotype, single lab\",\n      \"pmids\": [\"28671988\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Phosphorylation of TgCrk1 is altered in parasites depleted of the plant-like phosphatase PPKL, placing TgCrk1 downstream of PPKL in a signaling pathway that regulates daughter parasite development; global phosphoproteomics identified this change, and PPKL depletion phenocopies defects consistent with disrupted Crk1-dependent signaling.\",\n      \"method\": \"Conditional knockdown of PPKL, global phosphoproteomics, Co-immunoprecipitation and proximity labeling\",\n      \"journal\": \"bioRxiv : the preprint server for biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — phosphoproteomics identified altered Crk1 phosphorylation but direct mechanistic link (writer/eraser identity, specific sites, functional rescue) not established; preprint single lab\",\n      \"pmids\": [\"37398039\"],\n      \"is_preprint\": true,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Phosphorylation of TgCrk1 is altered in PPKL-depleted parasites, suggesting PPKL regulates the Crk1-dependent signaling pathway controlling daughter cell assembly; this was corroborated in the peer-reviewed publication of the same work.\",\n      \"method\": \"Conditional knockdown of PPKL with global phosphoproteomics\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — phosphoproteomics association, no direct biochemical reconstitution of PPKL acting on Crk1, single lab\",\n      \"pmids\": [\"37877735\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"TgCrk1 is a CDK-related kinase that forms a complex with the atypical cyclin TgCycL and is essential for daughter bud assembly during T. gondii tachyzoite endodyogeny; its activity is further regulated post-translationally, as its phosphorylation state is altered by the upstream plant-like phosphatase PPKL, placing TgCrk1 in a PPKL-dependent signaling pathway controlling daughter parasite development.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TgCrk1 is a CDK-related kinase that drives daughter bud assembly during Toxoplasma gondii tachyzoite endodyogeny [#0]. It functions in complex with the atypical cyclin TgCycL, and conditional depletion of TgCrk1 blocks daughter bud formation, establishing it as a mitotic kinase essential for cytokinesis [#0, #1]. TgCrk1 is embedded in a phosphatase-dependent regulatory pathway: its phosphorylation state is altered upon depletion of the plant-like phosphatase PPKL, placing TgCrk1 downstream of PPKL in signaling that controls daughter parasite development [#3]. Beyond this cyclin partnership and PPKL-dependent regulation, the substrates, specific phosphosites, and structural basis of TgCrk1 activity have not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Whether a CDK-related kinase governs the assembly of daughter parasites was unknown; identifying TgCrk1 as essential for bud formation established it as a mitotic kinase controlling tachyzoite cytokinesis.\",\n      \"evidence\": \"Conditional tet-OFF knockdown with quantitative fluorescence microscopy in T. gondii tachyzoites\",\n      \"pmids\": [\"28671988\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct kinase substrates driving bud assembly not identified\", \"No structural or catalytic characterization\", \"Activation mechanism of the kinase unresolved\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"The cyclin partner conferring specificity was unknown; Co-IP identified the atypical cyclin TgCycL as the binding partner, defining the functional TgCrk1-TgCycL complex.\",\n      \"evidence\": \"Co-immunoprecipitation with supporting genetic loss-of-function phenotype in T. gondii\",\n      \"pmids\": [\"28671988\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single Co-IP without reciprocal biochemical reconstitution\", \"Whether TgCycL activates TgCrk1 kinase activity not shown directly\", \"Stoichiometry and additional complex members unknown\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether TgCrk1 activity is regulated by upstream signaling was unknown; phosphoproteomics upon PPKL depletion showed altered TgCrk1 phosphorylation, placing the kinase in a PPKL-dependent pathway controlling daughter cell assembly.\",\n      \"evidence\": \"Conditional knockdown of PPKL with global phosphoproteomics, Co-IP and proximity labeling in T. gondii (initially bioRxiv preprint, corroborated in mBio)\",\n      \"pmids\": [\"37398039\", \"37877735\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct biochemical reconstitution of PPKL acting on TgCrk1\", \"Specific phosphosites and writer/eraser identity not established\", \"Functional rescue of TgCrk1 phosphostate not tested\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct substrates of TgCrk1, the phosphosites governing its activity, and the biochemical mechanism linking PPKL dephosphorylation to TgCrk1 function during endodyogeny remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No TgCrk1 substrate identified\", \"No direct enzyme-substrate reconstitution of the PPKL-TgCrk1 relationship\", \"No structural model of the TgCrk1-TgCycL complex\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004672\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0016538\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0000278\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0000910\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"TgCrk1-TgCycL kinase-cyclin complex\"],\n    \"partners\": [\"TgCycL (atypical cyclin)\", \"PPKL (plant-like phosphatase, upstream regulator)\"],\n    \"other_free_text\": [\n      \"TgCrk1 is a CDK-related kinase essential for daughter bud assembly during tachyzoite endodyogeny.\",\n      \"TgCrk1 phosphorylation state is altered upon PPKL depletion, placing it downstream of PPKL signaling.\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_304970","name":"CRK1","product":"CDK-related protein kinase CRK1","uniprot_acc":"A0A125YUD2","chromosome":"TGME49_chrIX","start_pos":5129987},{"strain":"GT1","gene_id":"TGGT1_304970","name":null,"product":"putative cell-cycle-associated protein kinase CDK","uniprot_acc":null,"chromosome":"TGGT1_chrIX","start_pos":4910810},{"strain":"RH88","gene_id":"TGRH88_016750","name":null,"product":"putative cell-cycle-associated protein kinase CDK","uniprot_acc":null,"chromosome":"CM023090","start_pos":5253185},{"strain":"VEG","gene_id":"TGVEG_304970","name":null,"product":"putative cell-cycle-associated protein kinase CDK","uniprot_acc":"B6KR18","chromosome":"TGVEG_chrIX","start_pos":5169138}]}