{"gene":"TG_261250","gene_symbol":"","run_date":"2026-09-08T12:58:25","timeline":{"discoveries":[{"year":2009,"finding":"Toxoplasma gondii H2A1 (canonical H2A) interacts with a novel H2B variant (H2Bv) as shown by co-immunoprecipitation; H2Bv does not interact with H2AX, indicating variant-specific nucleosome composition.","method":"Co-immunoprecipitation / protein interaction assay","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — reciprocal interaction established by co-IP in a single study, single lab, no in vitro reconstitution","pmids":["19607843"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2009,"finding":"H2A1 contains an SQ motif but lacks the complete SQ(E/D)φ motif required for DNA-damage-induced phosphorylation (unlike H2AX), indicating H2A1 is not the parasite's DNA-damage-responsive H2A variant.","method":"Sequence analysis with functional inference supported by DNA-damage phosphorylation assays on H2AX","journal":"Journal of molecular biology","confidence":"Low","confidence_rationale":"Tier 4 / Weak — conclusion based on sequence comparison; phosphorylation assay was performed on H2AX, not directly on H2A1","pmids":["19607843"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2009,"finding":"h2a1 transcription is upregulated in response to DNA damage in tachyzoites, but h2a1 expression is absent in mature bradyzoites arrested in G0 (in vivo), consistent with H2A1 being the replication-coupled canonical histone ortholog.","method":"RT-PCR / transcriptional analysis under DNA-damaging conditions and during stage differentiation (in vitro and in vivo bradyzoites)","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — stage-specific expression established by transcriptional assays across multiple conditions (DNA damage, in vitro and in vivo bradyzoites) in a single study","pmids":["19607843"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2020,"finding":"Recombinant TgH2A1 expressed in a prokaryotic system modulates murine macrophage functions, demonstrating a direct immunomodulatory activity of the protein.","method":"Prokaryotic recombinant protein expression, macrophage functional assays","journal":"Vaccines","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single study; macrophage modulation shown but molecular mechanism not defined","pmids":["33287313"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"Toxoplasma gondii H2A1 is the canonical, replication-coupled histone H2A that forms novel nucleosomes by interacting with a parasite-specific H2B variant (H2Bv) but not H2AX; its expression is restricted to actively dividing tachyzoites and is absent in quiescent bradyzoites, and it lacks the phosphorylatable SQ(E/D)φ motif that confers DNA-damage responsiveness to H2AX."},"narrative":{"mechanistic_narrative":"Toxoplasma gondii H2A1 is the parasite's replication-coupled canonical histone H2A, incorporated into nucleosomes during active tachyzoite division [PMID:19607843]. It assembles into a parasite-specific nucleosome by pairing with a novel H2B variant (H2Bv), a partnership established by co-immunoprecipitation; notably H2Bv does not interact with H2AX, marking H2A1–H2Bv as a distinct nucleosome composition [PMID:19607843]. Consistent with a canonical replication-linked histone rather than a DNA-damage-responsive variant, H2A1 carries an SQ motif but lacks the complete SQ(E/D)φ motif that confers damage-induced phosphorylation to H2AX, and its transcription rises upon DNA damage in dividing tachyzoites while its expression is absent in G0-arrested mature bradyzoites [PMID:19607843]. Beyond its chromatin role, recombinant TgH2A1 modulates murine macrophage functions, indicating an immunomodulatory activity distinct from its nucleosomal function, though the underlying molecular mechanism is undefined [PMID:33287313].","teleology":[{"year":2009,"claim":"It was unknown which H2B partner defines the parasite's canonical nucleosome; co-IP established that H2A1 partners with a novel H2B variant (H2Bv) and that this pairing is specific, since H2Bv does not bind H2AX.","evidence":"Co-immunoprecipitation / protein interaction assay in T. gondii","pmids":["19607843"],"confidence":"Medium","gaps":["No in vitro nucleosome reconstitution","Single lab, single study; reciprocal validation limited","Stoichiometry and structure of the H2A1–H2Bv nucleosome undefined"],"attribution":[]},{"year":2009,"claim":"It was unclear whether H2A1 or H2AX serves as the parasite's DNA-damage-responsive histone; sequence analysis showed H2A1 lacks the complete SQ(E/D)φ motif, assigning the damage-sensing role to H2AX rather than H2A1.","evidence":"Sequence analysis with functional inference; phosphorylation assays performed on H2AX, not H2A1","pmids":["19607843"],"confidence":"Low","gaps":["Phosphorylation was assayed on H2AX, not directly on H2A1","H2A1 post-translational modifications not directly characterized"],"attribution":[]},{"year":2009,"claim":"The stage-specific role of H2A1 was undefined; transcriptional profiling showed h2a1 is upregulated by DNA damage in tachyzoites but absent in G0-arrested bradyzoites, establishing it as a replication-coupled canonical histone.","evidence":"RT-PCR / transcriptional analysis under DNA damage and during stage differentiation (in vitro and in vivo bradyzoites)","pmids":["19607843"],"confidence":"Medium","gaps":["Protein-level expression across stages not resolved","Mechanism coupling transcription to replication not defined"],"attribution":[]},{"year":2020,"claim":"It was unknown whether H2A1 has activity beyond chromatin; recombinant TgH2A1 was shown to modulate macrophage functions, revealing an immunomodulatory property.","evidence":"Prokaryotic recombinant protein expression and murine macrophage functional assays","pmids":["33287313"],"confidence":"Low","gaps":["Molecular mechanism of macrophage modulation undefined","Relevance to natural infection not established","Single lab, single study"],"attribution":[]},{"year":null,"claim":"The structural basis of the H2A1–H2Bv nucleosome, the direct in vivo modifications of H2A1, and the mechanism of its immunomodulatory activity remain open.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of the H2A1–H2Bv nucleosome","No defined receptor or pathway for macrophage modulation","Direct H2A1 PTM landscape uncharacterized"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["H2A1–H2Bv nucleosome"],"partners":["H2BV (NOVEL H2B VARIANT)"],"other_free_text":["Replication-coupled canonical histone: transcript upregulated by DNA damage in dividing tachyzoites, absent in G0-arrested bradyzoites [#2]","Lacks the complete SQ(E/D)φ motif of H2AX and is therefore not the DNA-damage-responsive H2A variant [#1]","Recombinant TgH2A1 modulates murine macrophage functions [#3]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"19607843","id":"PMC_19607843","title":"Toxoplasma H2A variants reveal novel insights into nucleosome composition and functions for this histone family.","date":"2009","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/19607843","citation_count":51,"is_preprint":false},{"pmid":"33287313","id":"PMC_33287313","title":"Modulation Effects of Toxoplasma gondii Histone H2A1 on Murine Macrophages and Encapsulation with Polymer as a Vaccine Candidate.","date":"2020","source":"Vaccines","url":"https://pubmed.ncbi.nlm.nih.gov/33287313","citation_count":6,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3520,"output_tokens":1014,"usd":0.012885,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5910,"output_tokens":2060,"usd":0.040525,"stage2_stop_reason":"end_turn"},"total_usd":0.05341,"stage1_batch_id":"msgbatch_01TEPNZ4MCzJ7xtsNwosiDRk","stage2_batch_id":"msgbatch_01FQShM7n1sfCr4pWTDShmki","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2009,\n      \"finding\": \"Toxoplasma gondii H2A1 (canonical H2A) interacts with a novel H2B variant (H2Bv) as shown by co-immunoprecipitation; H2Bv does not interact with H2AX, indicating variant-specific nucleosome composition.\",\n      \"method\": \"Co-immunoprecipitation / protein interaction assay\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — reciprocal interaction established by co-IP in a single study, single lab, no in vitro reconstitution\",\n      \"pmids\": [\"19607843\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"H2A1 contains an SQ motif but lacks the complete SQ(E/D)φ motif required for DNA-damage-induced phosphorylation (unlike H2AX), indicating H2A1 is not the parasite's DNA-damage-responsive H2A variant.\",\n      \"method\": \"Sequence analysis with functional inference supported by DNA-damage phosphorylation assays on H2AX\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — conclusion based on sequence comparison; phosphorylation assay was performed on H2AX, not directly on H2A1\",\n      \"pmids\": [\"19607843\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"h2a1 transcription is upregulated in response to DNA damage in tachyzoites, but h2a1 expression is absent in mature bradyzoites arrested in G0 (in vivo), consistent with H2A1 being the replication-coupled canonical histone ortholog.\",\n      \"method\": \"RT-PCR / transcriptional analysis under DNA-damaging conditions and during stage differentiation (in vitro and in vivo bradyzoites)\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — stage-specific expression established by transcriptional assays across multiple conditions (DNA damage, in vitro and in vivo bradyzoites) in a single study\",\n      \"pmids\": [\"19607843\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Recombinant TgH2A1 expressed in a prokaryotic system modulates murine macrophage functions, demonstrating a direct immunomodulatory activity of the protein.\",\n      \"method\": \"Prokaryotic recombinant protein expression, macrophage functional assays\",\n      \"journal\": \"Vaccines\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single study; macrophage modulation shown but molecular mechanism not defined\",\n      \"pmids\": [\"33287313\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"Toxoplasma gondii H2A1 is the canonical, replication-coupled histone H2A that forms novel nucleosomes by interacting with a parasite-specific H2B variant (H2Bv) but not H2AX; its expression is restricted to actively dividing tachyzoites and is absent in quiescent bradyzoites, and it lacks the phosphorylatable SQ(E/D)φ motif that confers DNA-damage responsiveness to H2AX.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"Toxoplasma gondii H2A1 is the parasite's replication-coupled canonical histone H2A, incorporated into nucleosomes during active tachyzoite division [#2]. It assembles into a parasite-specific nucleosome by pairing with a novel H2B variant (H2Bv), a partnership established by co-immunoprecipitation; notably H2Bv does not interact with H2AX, marking H2A1–H2Bv as a distinct nucleosome composition [#0]. Consistent with a canonical replication-linked histone rather than a DNA-damage-responsive variant, H2A1 carries an SQ motif but lacks the complete SQ(E/D)\\u03c6 motif that confers damage-induced phosphorylation to H2AX, and its transcription rises upon DNA damage in dividing tachyzoites while its expression is absent in G0-arrested mature bradyzoites [#1, #2]. Beyond its chromatin role, recombinant TgH2A1 modulates murine macrophage functions, indicating an immunomodulatory activity distinct from its nucleosomal function, though the underlying molecular mechanism is undefined [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"It was unknown which H2B partner defines the parasite's canonical nucleosome; co-IP established that H2A1 partners with a novel H2B variant (H2Bv) and that this pairing is specific, since H2Bv does not bind H2AX.\",\n      \"evidence\": \"Co-immunoprecipitation / protein interaction assay in T. gondii\",\n      \"pmids\": [\"19607843\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vitro nucleosome reconstitution\", \"Single lab, single study; reciprocal validation limited\", \"Stoichiometry and structure of the H2A1\\u2013H2Bv nucleosome undefined\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"It was unclear whether H2A1 or H2AX serves as the parasite's DNA-damage-responsive histone; sequence analysis showed H2A1 lacks the complete SQ(E/D)\\u03c6 motif, assigning the damage-sensing role to H2AX rather than H2A1.\",\n      \"evidence\": \"Sequence analysis with functional inference; phosphorylation assays performed on H2AX, not H2A1\",\n      \"pmids\": [\"19607843\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Phosphorylation was assayed on H2AX, not directly on H2A1\", \"H2A1 post-translational modifications not directly characterized\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"The stage-specific role of H2A1 was undefined; transcriptional profiling showed h2a1 is upregulated by DNA damage in tachyzoites but absent in G0-arrested bradyzoites, establishing it as a replication-coupled canonical histone.\",\n      \"evidence\": \"RT-PCR / transcriptional analysis under DNA damage and during stage differentiation (in vitro and in vivo bradyzoites)\",\n      \"pmids\": [\"19607843\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Protein-level expression across stages not resolved\", \"Mechanism coupling transcription to replication not defined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"It was unknown whether H2A1 has activity beyond chromatin; recombinant TgH2A1 was shown to modulate macrophage functions, revealing an immunomodulatory property.\",\n      \"evidence\": \"Prokaryotic recombinant protein expression and murine macrophage functional assays\",\n      \"pmids\": [\"33287313\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Molecular mechanism of macrophage modulation undefined\", \"Relevance to natural infection not established\", \"Single lab, single study\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis of the H2A1\\u2013H2Bv nucleosome, the direct in vivo modifications of H2A1, and the mechanism of its immunomodulatory activity remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of the H2A1\\u2013H2Bv nucleosome\", \"No defined receptor or pathway for macrophage modulation\", \"Direct H2A1 PTM landscape uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0030527\", \"supporting_discovery_ids\": [0, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0042803\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0000786\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006334\", \"supporting_discovery_ids\": [0, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"H2A1\\u2013H2Bv nucleosome\"],\n    \"partners\": [\"H2Bv (novel H2B variant)\"],\n    \"other_free_text\": [\n      \"Replication-coupled canonical histone: transcript upregulated by DNA damage in dividing tachyzoites, absent in G0-arrested bradyzoites [#2]\",\n      \"Lacks the complete SQ(E/D)\\u03c6 motif of H2AX and is therefore not the DNA-damage-responsive H2A variant [#1]\",\n      \"Recombinant TgH2A1 modulates murine macrophage functions [#3]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_261250","name":null,"product":"histone H2A1","uniprot_acc":"A0A125YX75","chromosome":"TGME49_chrVIIb","start_pos":1806175},{"strain":"GT1","gene_id":"TGGT1_261250","name":null,"product":"histone H2A1","uniprot_acc":null,"chromosome":"TGGT1_chrVIIb","start_pos":1779724},{"strain":"RH88","gene_id":"TGRH88_069350","name":null,"product":"histone H2A1","uniprot_acc":null,"chromosome":"CM023089","start_pos":1825333},{"strain":"VEG","gene_id":"TGVEG_261250","name":null,"product":"histone H2A1","uniprot_acc":"A0A125YX76","chromosome":"TGVEG_chrVIIb","start_pos":1821751}]}