{"gene":"TG_301010","gene_symbol":"PP6C","run_date":"2026-09-08T15:15:12","timeline":{"discoveries":[{"year":2023,"finding":"TgPP6C (catalytic subunit) and TgPP6R (regulatory subunit) likely form a protein phosphatase 6 complex in T. gondii, whereas the predicted structural subunit TgPP6S does not co-assemble with TgPP6C and TgPP6R.","method":"Co-immunoprecipitation / complex assembly assay","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, single Co-IP method establishing complex composition; abstract uses 'likely' for TgPP6C–TgPP6R interaction but reports negative result for TgPP6S co-assembly as a direct experimental finding","pmids":["38091362"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2023,"finding":"TgPP6S does not co-assemble with TgPP6C and TgPP6R, indicating it is not part of the canonical TgPP6 holoenzyme complex.","method":"Co-immunoprecipitation / complex assembly assay (negative result)","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, single method; negative result is directly reported and mechanistically informative","pmids":["38091362"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2023,"finding":"Ablation of TgPP6C is essential for parasite growth and replication; its loss significantly reduces synchronous daughter-cell division during endodyogeny, resulting in disordered rosettes.","method":"Conditional knockdown / knockout with phenotypic analysis of endodyogeny","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean conditional ablation with defined cellular phenotype (disordered rosettes, impaired endodyogeny), single lab but multiple orthogonal readouts (growth assay, morphology, cell cycle)","pmids":["38091362"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2023,"finding":"The six conserved catalytic motifs of TgPP6C are required for efficient endodyogeny, establishing that phosphatase catalytic activity is necessary for cell division.","method":"Site-directed mutagenesis of conserved motifs combined with endodyogeny phenotypic assay","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 1 / Moderate — active-site mutagenesis with defined functional phenotype, single lab","pmids":["38091362"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2023,"finding":"Phosphoproteomic analysis after TgPP6C ablation revealed that TgPP6C predominantly controls the phosphorylation status of proteins involved in cell cycle regulation, placing TgPP6C as a phosphatase that dephosphorylates cell cycle regulators.","method":"Quantitative phosphoproteomics following conditional TgPP6C ablation","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — phosphoproteomics is a rigorous method but single lab; substrates are identified by altered phosphorylation status rather than direct dephosphorylation assay","pmids":["38091362"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2023,"finding":"Deletion of TgPP6C significantly attenuated parasite virulence in mice, demonstrating that TgPP6C is required for full pathogenicity in vivo.","method":"Mouse infection model with TgPP6C-deficient type I RH strain","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean KO with defined in vivo phenotype (attenuation), single lab","pmids":["38091362"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]}],"current_model":"TgPP6C is the catalytic subunit of the T. gondii protein phosphatase 6 complex (with regulatory subunit TgPP6R but not structural subunit TgPP6S), whose phosphatase activity—dependent on six conserved catalytic motifs—dephosphorylates cell cycle regulatory proteins to coordinate synchronous daughter-cell formation during endodyogeny, making it essential for parasite replication and virulence."},"narrative":{"mechanistic_narrative":"TgPP6C is the catalytic subunit of the Toxoplasma gondii protein phosphatase 6 complex that coordinates synchronous daughter-cell formation during endodyogeny [PMID:38091362]. It assembles with the regulatory subunit TgPP6R into a holoenzyme, whereas the predicted structural subunit TgPP6S does not co-assemble with TgPP6C and TgPP6R [PMID:38091362]. Its phosphatase activity depends on six conserved catalytic motifs required for efficient endodyogeny, and phosphoproteomics after TgPP6C ablation shows it predominantly controls the phosphorylation status of cell cycle regulatory proteins [PMID:38091362]. In the type I RH strain, TgPP6C is essential for parasite growth and replication—its loss impairs synchronous division and produces disordered rosettes—and is required for full virulence in mice [PMID:38091362]. Direct dephosphorylation of individual substrates has not been demonstrated in the available corpus.","teleology":[{"year":2023,"claim":"Defining the composition of the T. gondii PP6 complex established that TgPP6C partners with the regulatory subunit TgPP6R but not with the predicted structural subunit TgPP6S, refining the holoenzyme architecture.","evidence":"Co-immunoprecipitation / complex assembly assay in RH strain","pmids":["38091362"],"confidence":"Medium","gaps":["TgPP6C–TgPP6R interaction reported as 'likely' from a single Co-IP without reciprocal validation","stoichiometry and structural basis of assembly not resolved","reason TgPP6S fails to co-assemble not determined"],"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2023,"claim":"Conditional ablation showed TgPP6C is essential for parasite growth and that its loss disrupts synchronous daughter-cell division, placing the phosphatase at the heart of endodyogeny coordination.","evidence":"Conditional knockdown/knockout with growth, morphology, and cell cycle readouts in RH strain","pmids":["38091362"],"confidence":"High","gaps":["mechanistic link between phosphatase loss and rosette disorder not defined","cell cycle stage of the block not pinpointed"],"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2023,"claim":"Mutagenesis of the six conserved catalytic motifs demonstrated that catalytic phosphatase activity, not merely the protein's scaffolding, is required for efficient endodyogeny.","evidence":"Site-directed mutagenesis of catalytic motifs plus endodyogeny phenotype in RH strain","pmids":["38091362"],"confidence":"High","gaps":["individual contributions of each motif not dissected","residual activity of mutants not quantified"],"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2023,"claim":"Phosphoproteomics after ablation identified cell cycle regulators as the predominant class of proteins whose phosphorylation TgPP6C controls, providing the substrate landscape for its division role.","evidence":"Quantitative phosphoproteomics following conditional ablation in RH strain","pmids":["38091362"],"confidence":"Medium","gaps":["substrates inferred from altered phosphorylation, not direct dephosphorylation assays","no individual substrate validated in vitro","direct vs indirect effects not distinguished"],"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":2023,"claim":"Deletion in the type I RH strain attenuated virulence in mice, connecting the replication defect to a requirement for full in vivo pathogenicity.","evidence":"Mouse infection model with TgPP6C-deficient RH strain","pmids":["38091362"],"confidence":"Medium","gaps":["not tested in other strains or acute/chronic stages","whether attenuation is solely from replication defect not established"],"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]},{"year":null,"claim":"Direct enzyme-substrate relationships and the biochemical mechanism by which TgPP6C dephosphorylation coordinates daughter-cell formation remain to be defined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["no direct dephosphorylation assay for any candidate substrate","role of TgPP6R in substrate targeting unknown","structural model of holoenzyme absent"],"attribution":[{"species":"Toxoplasma gondii","strain":"RH"}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Protein phosphatase 6 holoenzyme (TgPP6C catalytic + TgPP6R regulatory subunit)"],"partners":["TGPP6R (REGULATORY SUBUNIT)"],"other_free_text":["TgPP6S (predicted structural subunit) does not co-assemble with TgPP6C/TgPP6R [#1]","Essential for parasite growth and synchronous endodyogeny; loss produces disordered rosettes [#2]","Required for full virulence in mice (type I RH strain) [#5]","Phosphatase activity depends on six conserved catalytic motifs [#3]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"38091362","id":"PMC_38091362","title":"The Toxoplasma protein phosphatase 6 catalytic subunit (TgPP6C) is essential for cell cycle progression and virulence.","date":"2023","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/38091362","citation_count":11,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2973,"output_tokens":1408,"usd":0.015019,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6483,"output_tokens":2297,"usd":0.04492,"stage2_stop_reason":"end_turn"},"total_usd":0.059939,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"TgPP6C (catalytic subunit) and TgPP6R (regulatory subunit) likely form a protein phosphatase 6 complex in T. gondii, whereas the predicted structural subunit TgPP6S does not co-assemble with TgPP6C and TgPP6R.\",\n      \"method\": \"Co-immunoprecipitation / complex assembly assay\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, single Co-IP method establishing complex composition; abstract uses 'likely' for TgPP6C–TgPP6R interaction but reports negative result for TgPP6S co-assembly as a direct experimental finding\",\n      \"pmids\": [\"38091362\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TgPP6S does not co-assemble with TgPP6C and TgPP6R, indicating it is not part of the canonical TgPP6 holoenzyme complex.\",\n      \"method\": \"Co-immunoprecipitation / complex assembly assay (negative result)\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, single method; negative result is directly reported and mechanistically informative\",\n      \"pmids\": [\"38091362\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Ablation of TgPP6C is essential for parasite growth and replication; its loss significantly reduces synchronous daughter-cell division during endodyogeny, resulting in disordered rosettes.\",\n      \"method\": \"Conditional knockdown / knockout with phenotypic analysis of endodyogeny\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean conditional ablation with defined cellular phenotype (disordered rosettes, impaired endodyogeny), single lab but multiple orthogonal readouts (growth assay, morphology, cell cycle)\",\n      \"pmids\": [\"38091362\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The six conserved catalytic motifs of TgPP6C are required for efficient endodyogeny, establishing that phosphatase catalytic activity is necessary for cell division.\",\n      \"method\": \"Site-directed mutagenesis of conserved motifs combined with endodyogeny phenotypic assay\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — active-site mutagenesis with defined functional phenotype, single lab\",\n      \"pmids\": [\"38091362\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Phosphoproteomic analysis after TgPP6C ablation revealed that TgPP6C predominantly controls the phosphorylation status of proteins involved in cell cycle regulation, placing TgPP6C as a phosphatase that dephosphorylates cell cycle regulators.\",\n      \"method\": \"Quantitative phosphoproteomics following conditional TgPP6C ablation\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — phosphoproteomics is a rigorous method but single lab; substrates are identified by altered phosphorylation status rather than direct dephosphorylation assay\",\n      \"pmids\": [\"38091362\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Deletion of TgPP6C significantly attenuated parasite virulence in mice, demonstrating that TgPP6C is required for full pathogenicity in vivo.\",\n      \"method\": \"Mouse infection model with TgPP6C-deficient type I RH strain\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean KO with defined in vivo phenotype (attenuation), single lab\",\n      \"pmids\": [\"38091362\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    }\n  ],\n  \"current_model\": \"TgPP6C is the catalytic subunit of the T. gondii protein phosphatase 6 complex (with regulatory subunit TgPP6R but not structural subunit TgPP6S), whose phosphatase activity—dependent on six conserved catalytic motifs—dephosphorylates cell cycle regulatory proteins to coordinate synchronous daughter-cell formation during endodyogeny, making it essential for parasite replication and virulence.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TgPP6C is the catalytic subunit of the Toxoplasma gondii protein phosphatase 6 complex that coordinates synchronous daughter-cell formation during endodyogeny [#2, #4]. It assembles with the regulatory subunit TgPP6R into a holoenzyme, whereas the predicted structural subunit TgPP6S does not co-assemble with TgPP6C and TgPP6R [#0, #1]. Its phosphatase activity depends on six conserved catalytic motifs required for efficient endodyogeny, and phosphoproteomics after TgPP6C ablation shows it predominantly controls the phosphorylation status of cell cycle regulatory proteins [#3, #4]. In the type I RH strain, TgPP6C is essential for parasite growth and replication\\u2014its loss impairs synchronous division and produces disordered rosettes\\u2014and is required for full virulence in mice [#2, #5]. Direct dephosphorylation of individual substrates has not been demonstrated in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Defining the composition of the T. gondii PP6 complex established that TgPP6C partners with the regulatory subunit TgPP6R but not with the predicted structural subunit TgPP6S, refining the holoenzyme architecture.\",\n      \"evidence\": \"Co-immunoprecipitation / complex assembly assay in RH strain\",\n      \"pmids\": [\"38091362\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"TgPP6C\\u2013TgPP6R interaction reported as 'likely' from a single Co-IP without reciprocal validation\", \"stoichiometry and structural basis of assembly not resolved\", \"reason TgPP6S fails to co-assemble not determined\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Conditional ablation showed TgPP6C is essential for parasite growth and that its loss disrupts synchronous daughter-cell division, placing the phosphatase at the heart of endodyogeny coordination.\",\n      \"evidence\": \"Conditional knockdown/knockout with growth, morphology, and cell cycle readouts in RH strain\",\n      \"pmids\": [\"38091362\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"mechanistic link between phosphatase loss and rosette disorder not defined\", \"cell cycle stage of the block not pinpointed\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Mutagenesis of the six conserved catalytic motifs demonstrated that catalytic phosphatase activity, not merely the protein's scaffolding, is required for efficient endodyogeny.\",\n      \"evidence\": \"Site-directed mutagenesis of catalytic motifs plus endodyogeny phenotype in RH strain\",\n      \"pmids\": [\"38091362\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"individual contributions of each motif not dissected\", \"residual activity of mutants not quantified\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Phosphoproteomics after ablation identified cell cycle regulators as the predominant class of proteins whose phosphorylation TgPP6C controls, providing the substrate landscape for its division role.\",\n      \"evidence\": \"Quantitative phosphoproteomics following conditional ablation in RH strain\",\n      \"pmids\": [\"38091362\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"substrates inferred from altered phosphorylation, not direct dephosphorylation assays\", \"no individual substrate validated in vitro\", \"direct vs indirect effects not distinguished\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Deletion in the type I RH strain attenuated virulence in mice, connecting the replication defect to a requirement for full in vivo pathogenicity.\",\n      \"evidence\": \"Mouse infection model with TgPP6C-deficient RH strain\",\n      \"pmids\": [\"38091362\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"not tested in other strains or acute/chronic stages\", \"whether attenuation is solely from replication defect not established\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Direct enzyme-substrate relationships and the biochemical mechanism by which TgPP6C dephosphorylation coordinates daughter-cell formation remain to be defined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"no direct dephosphorylation assay for any candidate substrate\", \"role of TgPP6R in substrate targeting unknown\", \"structural model of holoenzyme absent\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004722\", \"supporting_discovery_ids\": [3, 4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0051301\", \"supporting_discovery_ids\": [2, 4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]},\n      {\"term_id\": \"GO:0007049\", \"supporting_discovery_ids\": [4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}]}\n    ],\n    \"complexes\": [\"Protein phosphatase 6 holoenzyme (TgPP6C catalytic + TgPP6R regulatory subunit)\"],\n    \"partners\": [\"TgPP6R (regulatory subunit)\"],\n    \"other_free_text\": [\n      \"TgPP6S (predicted structural subunit) does not co-assemble with TgPP6C/TgPP6R [#1]\",\n      \"Essential for parasite growth and synchronous endodyogeny; loss produces disordered rosettes [#2]\",\n      \"Required for full virulence in mice (type I RH strain) [#5]\",\n      \"Phosphatase activity depends on six conserved catalytic motifs [#3]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_301010","name":"PP6C","product":"serine/threonine protein phosphatase 6 catalytic subunit PP6C","uniprot_acc":"A0A125YRR5","chromosome":"TGME49_chrIV","start_pos":2266611},{"strain":"GT1","gene_id":"TGGT1_301010","name":null,"product":"putative serine/threonine protein phosphatase","uniprot_acc":null,"chromosome":"TGGT1_chrIV","start_pos":2154537},{"strain":"RH88","gene_id":"TGRH88_009900","name":null,"product":"putative serine/threonine protein phosphatase","uniprot_acc":null,"chromosome":"CM023085","start_pos":2640552},{"strain":"VEG","gene_id":"TGVEG_301010","name":null,"product":"putative serine/threonine protein phosphatase","uniprot_acc":"B9QQ26","chromosome":"TGVEG_chrIV","start_pos":2300038}]}