{"gene":"TG_267100","gene_symbol":"PPM2B","run_date":"2026-09-08T14:08:29","timeline":{"discoveries":[{"year":2024,"finding":"PPM2B is a phosphatase 2C domain-containing serine/threonine phosphatase (PPM family) that localizes mainly to the cytoplasm of T. gondii tachyzoites, as determined by insertion of a 10HA tag at the C-terminus.","method":"Endogenous C-terminal 10HA tagging and localization by immunofluorescence in RH∆ku80 strain","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization experiment with epitope tag, single lab, single method","pmids":["39461506"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH∆ku80"}]},{"year":2024,"finding":"PPM2B knockout (Δppm2b) in T. gondii does not cause an intracellular replication defect, and single or double knockout of PPM2A/PPM2B does not reduce pathogenicity in mice compared to the RH∆hxgprt control.","method":"CRISPR-Cas9 knockout, intracellular replication assay, and mouse virulence experiments","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined cellular and in vivo phenotypic readouts, single lab, two orthogonal assays (in vitro replication + mouse experiment), but finding is negative (no replication defect, no virulence reduction)","pmids":["39461506"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH∆hxgprt"}]},{"year":2024,"finding":"PPM2B knockout results in smaller plaque size compared to the RH∆hxgprt control strain, indicating a role for PPM2B in parasite fitness or growth efficiency even though intracellular replication per se is not impaired.","method":"Plaque assay comparing Δppm2b and double-knockout strains to RH∆hxgprt control","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — loss-of-function plaque assay with defined phenotypic readout, single lab, single method","pmids":["39461506"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH∆hxgprt"}]}],"current_model":"PPM2B is a cytoplasm-localized PPM-family serine/threonine phosphatase in T. gondii tachyzoites whose loss does not impair intracellular replication or mouse virulence but reduces plaque size, indicating a role in parasite fitness rather than essential replication or acute pathogenesis."},"narrative":{"mechanistic_narrative":"PPM2B is a PPM (protein phosphatase 2C)-family serine/threonine phosphatase of Toxoplasma gondii that localizes mainly to the tachyzoite cytoplasm [PMID:39461506]. Genetic ablation of PPM2B does not impair intracellular replication, and neither single knockout nor combined PPM2A/PPM2B double knockout reduces virulence in mice, indicating the phosphatase is dispensable for essential replication and acute pathogenesis [PMID:39461506]. Its loss does, however, reduce plaque size relative to control parasites, assigning PPM2B a role in overall parasite fitness or growth efficiency rather than in the replication cycle itself [PMID:39461506]. Beyond these localization and loss-of-function observations, no substrates, interacting partners, or catalytic mechanism have been characterized in the available corpus.","teleology":[{"year":2024,"claim":"Establishing where PPM2B acts was the first step in assigning function; endogenous tagging placed this PPM-family phosphatase in the tachyzoite cytoplasm.","evidence":"Endogenous C-terminal 10HA tagging with immunofluorescence localization in RHΔku80","pmids":["39461506"],"confidence":"Medium","gaps":["No substrates or dephosphorylation targets identified","Catalytic activity not directly demonstrated in vitro","No interacting partners defined"],"attribution":[{"species":"Toxoplasma gondii","strain":"RHΔku80"}]},{"year":2024,"claim":"To test whether PPM2B is required for parasite propagation and disease, knockouts were assessed, showing the phosphatase is dispensable for intracellular replication and acute virulence.","evidence":"CRISPR-Cas9 knockout with intracellular replication assay and mouse virulence experiments, including PPM2A/PPM2B double knockout, versus RHΔhxgprt control","pmids":["39461506"],"confidence":"Medium","gaps":["Negative in vivo result does not exclude a role under other conditions or in chronic/cyst stages","Possible functional redundancy with other phosphatases not fully excluded despite the double knockout","Molecular basis of dispensability unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":"RHΔhxgprt"}]},{"year":2024,"claim":"A subtler phenotype was sought to reconcile the absence of a replication defect; plaque assays revealed reduced plaque size, implicating PPM2B in parasite fitness rather than the replication cycle per se.","evidence":"Plaque assay comparing Δppm2b and double-knockout strains to RHΔhxgprt control","pmids":["39461506"],"confidence":"Medium","gaps":["Which step of the lytic cycle (invasion, egress, motility) underlies the plaque defect is unresolved","The signaling pathway or substrate linking PPM2B to growth efficiency is unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":"RHΔhxgprt"}]},{"year":null,"claim":"The physiological substrates, catalytic activity, and the molecular basis of the fitness defect for PPM2B remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No substrate or interactome identified","Mechanistic link between phosphatase activity and reduced plaque size undefined","Function in non-RH strains and chronic stages uncharacterized"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":["PPM (protein phosphatase 2C) family serine/threonine phosphatase containing a phosphatase 2C domain [#0]","Dispensable for intracellular replication and for acute virulence in mice, individually and in PPM2A/PPM2B double knockout [#1]","Loss reduces plaque size, indicating a role in parasite fitness/growth efficiency rather than essential replication [#2]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"39461506","id":"PMC_39461506","title":"Characterization of two phosphatase 2 C domain-containing proteins PPM2A and PPM2B in Toxoplasma gondii.","date":"2024","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/39461506","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2974,"output_tokens":848,"usd":0.010821,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5620,"output_tokens":1763,"usd":0.036088,"stage2_stop_reason":"end_turn"},"total_usd":0.046909,"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\": 2024,\n      \"finding\": \"PPM2B is a phosphatase 2C domain-containing serine/threonine phosphatase (PPM family) that localizes mainly to the cytoplasm of T. gondii tachyzoites, as determined by insertion of a 10HA tag at the C-terminus.\",\n      \"method\": \"Endogenous C-terminal 10HA tagging and localization by immunofluorescence in RH∆ku80 strain\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization experiment with epitope tag, single lab, single method\",\n      \"pmids\": [\"39461506\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"RH∆ku80\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PPM2B knockout (Δppm2b) in T. gondii does not cause an intracellular replication defect, and single or double knockout of PPM2A/PPM2B does not reduce pathogenicity in mice compared to the RH∆hxgprt control.\",\n      \"method\": \"CRISPR-Cas9 knockout, intracellular replication assay, and mouse virulence experiments\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined cellular and in vivo phenotypic readouts, single lab, two orthogonal assays (in vitro replication + mouse experiment), but finding is negative (no replication defect, no virulence reduction)\",\n      \"pmids\": [\"39461506\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"RH∆hxgprt\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PPM2B knockout results in smaller plaque size compared to the RH∆hxgprt control strain, indicating a role for PPM2B in parasite fitness or growth efficiency even though intracellular replication per se is not impaired.\",\n      \"method\": \"Plaque assay comparing Δppm2b and double-knockout strains to RH∆hxgprt control\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — loss-of-function plaque assay with defined phenotypic readout, single lab, single method\",\n      \"pmids\": [\"39461506\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"RH∆hxgprt\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PPM2B is a cytoplasm-localized PPM-family serine/threonine phosphatase in T. gondii tachyzoites whose loss does not impair intracellular replication or mouse virulence but reduces plaque size, indicating a role in parasite fitness rather than essential replication or acute pathogenesis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PPM2B is a PPM (protein phosphatase 2C)-family serine/threonine phosphatase of Toxoplasma gondii that localizes mainly to the tachyzoite cytoplasm [#0]. Genetic ablation of PPM2B does not impair intracellular replication, and neither single knockout nor combined PPM2A/PPM2B double knockout reduces virulence in mice, indicating the phosphatase is dispensable for essential replication and acute pathogenesis [#1]. Its loss does, however, reduce plaque size relative to control parasites, assigning PPM2B a role in overall parasite fitness or growth efficiency rather than in the replication cycle itself [#2]. Beyond these localization and loss-of-function observations, no substrates, interacting partners, or catalytic mechanism have been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2024,\n      \"claim\": \"Establishing where PPM2B acts was the first step in assigning function; endogenous tagging placed this PPM-family phosphatase in the tachyzoite cytoplasm.\",\n      \"evidence\": \"Endogenous C-terminal 10HA tagging with immunofluorescence localization in RH\\u0394ku80\",\n      \"pmids\": [\"39461506\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No substrates or dephosphorylation targets identified\",\n        \"Catalytic activity not directly demonstrated in vitro\",\n        \"No interacting partners defined\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\\u0394ku80\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"To test whether PPM2B is required for parasite propagation and disease, knockouts were assessed, showing the phosphatase is dispensable for intracellular replication and acute virulence.\",\n      \"evidence\": \"CRISPR-Cas9 knockout with intracellular replication assay and mouse virulence experiments, including PPM2A/PPM2B double knockout, versus RH\\u0394hxgprt control\",\n      \"pmids\": [\"39461506\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Negative in vivo result does not exclude a role under other conditions or in chronic/cyst stages\",\n        \"Possible functional redundancy with other phosphatases not fully excluded despite the double knockout\",\n        \"Molecular basis of dispensability unknown\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\\u0394hxgprt\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A subtler phenotype was sought to reconcile the absence of a replication defect; plaque assays revealed reduced plaque size, implicating PPM2B in parasite fitness rather than the replication cycle per se.\",\n      \"evidence\": \"Plaque assay comparing \\u0394ppm2b and double-knockout strains to RH\\u0394hxgprt control\",\n      \"pmids\": [\"39461506\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Which step of the lytic cycle (invasion, egress, motility) underlies the plaque defect is unresolved\",\n        \"The signaling pathway or substrate linking PPM2B to growth efficiency is unknown\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\\u0394hxgprt\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The physiological substrates, catalytic activity, and the molecular basis of the fitness defect for PPM2B remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No substrate or interactome identified\",\n        \"Mechanistic link between phosphatase activity and reduced plaque size undefined\",\n        \"Function in non-RH strains and chronic stages uncharacterized\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004722\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\\u0394ku80\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005737\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\\u0394ku80\"}]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"PPM (protein phosphatase 2C) family serine/threonine phosphatase containing a phosphatase 2C domain [#0]\",\n      \"Dispensable for intracellular replication and for acute virulence in mice, individually and in PPM2A/PPM2B double knockout [#1]\",\n      \"Loss reduces plaque size, indicating a role in parasite fitness/growth efficiency rather than essential replication [#2]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_267100","name":"PPM2B","product":"protein phosphatase PPM2B","uniprot_acc":"S8F273","chromosome":"TGME49_chrIX","start_pos":774868},{"strain":"GT1","gene_id":"TGGT1_267100","name":null,"product":"protein phosphatase 2C domain-containing protein","uniprot_acc":null,"chromosome":"TGGT1_chrIX","start_pos":612107},{"strain":"RH88","gene_id":"TGRH88_010920","name":null,"product":"protein phosphatase 2C domain-containing protein","uniprot_acc":null,"chromosome":"CM023090","start_pos":824805},{"strain":"VEG","gene_id":"TGVEG_267100","name":null,"product":"protein phosphatase 2C domain-containing protein","uniprot_acc":"B9QP93","chromosome":"TGVEG_chrIX","start_pos":803022}]}