{"gene":"TG_249680","gene_symbol":"PAF1","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2014,"finding":"Toxoplasma gondii PAF1 (LEO1 polymerase-associated factor / Paf1 subunit) was identified as a component of the GCN5b acetyltransferase 'core complex' that includes the co-activator ADA2-A, TFIID subunits, LEO1/PAF1, and RRM proteins, as determined by proteomics studies of GCN5b co-immunoprecipitation.","method":"Co-immunoprecipitation followed by proteomics (mass spectrometry) of HA-tagged GCN5b","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single lab, single Co-IP/proteomics pulldown identifying PAF1 as a binding partner of GCN5b; no direct functional follow-up on PAF1 itself","pmids":["24391497"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"Toxoplasma gondii PAF1 (the LEO1/Paf1 polymerase-associated factor subunit) has been identified as a component of the GCN5b lysine acetyltransferase 'core complex' involved in transcriptional and chromatin remodeling, but no direct functional experiments on PAF1 itself have been reported in the available literature."},"narrative":{"mechanistic_narrative":"In Toxoplasma gondii, PAF1 (the LEO1/Paf1 polymerase-associated factor subunit) has been identified as a component of the GCN5b lysine acetyltransferase 'core complex', which also contains the co-activator ADA2-A, TFIID subunits, and RRM proteins, based on co-immunoprecipitation and proteomics of GCN5b [PMID:24391497]. This places PAF1 within a machinery linked to transcriptional and chromatin regulation, but no direct functional experiments on PAF1 itself have been reported in the available corpus.","teleology":[{"year":2014,"claim":"To define the composition of the GCN5b acetyltransferase machinery in Toxoplasma, this work established that PAF1/LEO1 associates with a GCN5b 'core complex' alongside ADA2-A, TFIID subunits, and RRM proteins, placing PAF1 in a transcription/chromatin-remodeling context.","evidence":"Co-immunoprecipitation of HA-tagged GCN5b followed by mass spectrometry proteomics in Toxoplasma gondii","pmids":["24391497"],"confidence":"Medium","gaps":["Single Co-IP/proteomics pulldown; no reciprocal PAF1 pulldown to confirm the interaction","No direct functional characterization of PAF1's role within the complex","Whether PAF1 is required for GCN5b activity, transcription, or parasite viability is untested"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"The molecular function of PAF1 itself, its requirement for GCN5b complex integrity or activity, and its role in transcription and chromatin regulation remain uncharacterized.","evidence":"No direct functional experiments on PAF1 reported in the available corpus","pmids":[],"confidence":"Medium","gaps":["No knockout or knockdown phenotype for PAF1","No demonstration of a direct enzymatic or regulatory activity","No structural or reciprocal interaction data"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["GCN5b acetyltransferase core complex"],"partners":["GCN5B","ADA2-A","TFIID SUBUNITS","RRM PROTEINS"],"other_free_text":["Identified as a GCN5b interactor by Co-IP/proteomics; no direct functional data on PAF1 itself [#0]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"27382155","id":"PMC_27382155","title":"Dendrimer-RNA nanoparticles generate protective immunity against lethal Ebola, H1N1 influenza, and Toxoplasma gondii challenges with a single dose.","date":"2016","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/27382155","citation_count":318,"is_preprint":false},{"pmid":"27213691","id":"PMC_27213691","title":"Id2 reinforces TH1 differentiation and inhibits E2A to repress TFH differentiation.","date":"2016","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/27213691","citation_count":100,"is_preprint":false},{"pmid":"24391497","id":"PMC_24391497","title":"Lysine acetyltransferase GCN5b interacts with AP2 factors and is required for Toxoplasma gondii proliferation.","date":"2014","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/24391497","citation_count":63,"is_preprint":false},{"pmid":"21685318","id":"PMC_21685318","title":"Protein arginine methylation in parasitic protozoa.","date":"2011","source":"Eukaryotic cell","url":"https://pubmed.ncbi.nlm.nih.gov/21685318","citation_count":50,"is_preprint":false},{"pmid":"16951324","id":"PMC_16951324","title":"Different neurotropic pathogens elicit neurotoxic CCR9- or neurosupportive CXCR3-expressing microglia.","date":"2006","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/16951324","citation_count":49,"is_preprint":false},{"pmid":"9561772","id":"PMC_9561772","title":"Phylogenetic analysis of coccidia based on 18S rDNA sequence comparison indicates that Isospora is most closely related to Toxoplasma and Neospora.","date":"1998","source":"The Journal of eukaryotic microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/9561772","citation_count":49,"is_preprint":false},{"pmid":"17172185","id":"PMC_17172185","title":"Comparison between two real-time PCR assays and a nested-PCR for the detection of Toxoplasma gondii.","date":"2006","source":"Acta bio-medica : Atenei Parmensis","url":"https://pubmed.ncbi.nlm.nih.gov/17172185","citation_count":49,"is_preprint":false},{"pmid":"1601300","id":"PMC_1601300","title":"Physical and genetic mapping of cloned ribosomal DNA from Toxoplasma gondii: primary and secondary structure of the 5S gene.","date":"1992","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/1601300","citation_count":48,"is_preprint":false},{"pmid":"29216332","id":"PMC_29216332","title":"Voltage-dependent calcium channel signaling mediates GABAA receptor-induced migratory activation of dendritic cells infected by Toxoplasma gondii.","date":"2017","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/29216332","citation_count":48,"is_preprint":false},{"pmid":"15845546","id":"PMC_15845546","title":"A novel class of dual-family immunophilins.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15845546","citation_count":47,"is_preprint":false},{"pmid":"28424680","id":"PMC_28424680","title":"Induction of Protective Immunity against Toxoplasma gondii in Mice by Nucleoside Triphosphate Hydrolase-II (NTPase-II) Self-amplifying RNA Vaccine Encapsulated in Lipid Nanoparticle (LNP).","date":"2017","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/28424680","citation_count":46,"is_preprint":false},{"pmid":"23196113","id":"PMC_23196113","title":"Evidence for a Single Origin of the 35 kb Plastid DNA in Apicomplexans.","date":"2009","source":"Protist","url":"https://pubmed.ncbi.nlm.nih.gov/23196113","citation_count":45,"is_preprint":false},{"pmid":"2710166","id":"PMC_2710166","title":"Cloning of cDNAs encoding a 28 kilodalton antigen of Toxoplasma gondii.","date":"1989","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/2710166","citation_count":45,"is_preprint":false},{"pmid":"5414249","id":"PMC_5414249","title":"The RNA of toxoplasma gondii.","date":"1970","source":"Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/5414249","citation_count":44,"is_preprint":false},{"pmid":"25444863","id":"PMC_25444863","title":"Knockout of leucine aminopeptidase in Toxoplasma gondii using CRISPR/Cas9.","date":"2014","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/25444863","citation_count":41,"is_preprint":false},{"pmid":"12711703","id":"PMC_12711703","title":"Pleiotropic effect due to targeted depletion of secretory rhoptry protein ROP2 in Toxoplasma gondii.","date":"2003","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/12711703","citation_count":41,"is_preprint":false},{"pmid":"9657328","id":"PMC_9657328","title":"Upstream elements required for expression of nucleoside triphosphate hydrolase genes of Toxoplasma gondii.","date":"1998","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/9657328","citation_count":41,"is_preprint":false},{"pmid":"33688018","id":"PMC_33688018","title":"Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites.","date":"2021","source":"mSystems","url":"https://pubmed.ncbi.nlm.nih.gov/33688018","citation_count":40,"is_preprint":false},{"pmid":"7970867","id":"PMC_7970867","title":"Temporal differences in the expression of mRNA for IL-10 and IFN-gamma in the brains and spleens of C57BL/10 mice infected with Toxoplasma gondii.","date":"1994","source":"Parasite immunology","url":"https://pubmed.ncbi.nlm.nih.gov/7970867","citation_count":39,"is_preprint":false},{"pmid":"4215743","id":"PMC_4215743","title":"Protection against Toxoplasma gondii in mice immunized with Toxoplasma cell fractions, RNA and synthetic polyribonucleotides.","date":"1974","source":"Immunology","url":"https://pubmed.ncbi.nlm.nih.gov/4215743","citation_count":38,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12830,"output_tokens":411,"usd":0.022328,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4989,"output_tokens":1015,"usd":0.02516,"stage2_stop_reason":"end_turn"},"total_usd":0.047488,"stage1_batch_id":"msgbatch_01TEPNZ4MCzJ7xtsNwosiDRk","stage2_batch_id":"msgbatch_01FQShM7n1sfCr4pWTDShmki","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\": 2014,\n      \"finding\": \"Toxoplasma gondii PAF1 (LEO1 polymerase-associated factor / Paf1 subunit) was identified as a component of the GCN5b acetyltransferase 'core complex' that includes the co-activator ADA2-A, TFIID subunits, LEO1/PAF1, and RRM proteins, as determined by proteomics studies of GCN5b co-immunoprecipitation.\",\n      \"method\": \"Co-immunoprecipitation followed by proteomics (mass spectrometry) of HA-tagged GCN5b\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single lab, single Co-IP/proteomics pulldown identifying PAF1 as a binding partner of GCN5b; no direct functional follow-up on PAF1 itself\",\n      \"pmids\": [\"24391497\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"Toxoplasma gondii PAF1 (the LEO1/Paf1 polymerase-associated factor subunit) has been identified as a component of the GCN5b lysine acetyltransferase 'core complex' involved in transcriptional and chromatin remodeling, but no direct functional experiments on PAF1 itself have been reported in the available literature.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"In Toxoplasma gondii, PAF1 (the LEO1/Paf1 polymerase-associated factor subunit) has been identified as a component of the GCN5b lysine acetyltransferase 'core complex', which also contains the co-activator ADA2-A, TFIID subunits, and RRM proteins, based on co-immunoprecipitation and proteomics of GCN5b [#0]. This places PAF1 within a machinery linked to transcriptional and chromatin regulation, but no direct functional experiments on PAF1 itself have been reported in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"To define the composition of the GCN5b acetyltransferase machinery in Toxoplasma, this work established that PAF1/LEO1 associates with a GCN5b 'core complex' alongside ADA2-A, TFIID subunits, and RRM proteins, placing PAF1 in a transcription/chromatin-remodeling context.\",\n      \"evidence\": \"Co-immunoprecipitation of HA-tagged GCN5b followed by mass spectrometry proteomics in Toxoplasma gondii\",\n      \"pmids\": [\"24391497\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single Co-IP/proteomics pulldown; no reciprocal PAF1 pulldown to confirm the interaction\",\n        \"No direct functional characterization of PAF1's role within the complex\",\n        \"Whether PAF1 is required for GCN5b activity, transcription, or parasite viability is untested\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular function of PAF1 itself, its requirement for GCN5b complex integrity or activity, and its role in transcription and chromatin regulation remain uncharacterized.\",\n      \"evidence\": \"No direct functional experiments on PAF1 reported in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No knockout or knockdown phenotype for PAF1\",\n        \"No demonstration of a direct enzymatic or regulatory activity\",\n        \"No structural or reciprocal interaction data\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [\"GCN5b acetyltransferase core complex\"],\n    \"partners\": [\"GCN5b\", \"ADA2-A\", \"TFIID subunits\", \"RRM proteins\"],\n    \"other_free_text\": [\n      \"Identified as a GCN5b interactor by Co-IP/proteomics; no direct functional data on PAF1 itself [#0]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_249680","name":"PAF1","product":"RNA polymerase II associated Paf1 complex component PAF1","uniprot_acc":"A0A125YK22","chromosome":"TGME49_chrXII","start_pos":4728287},{"strain":"GT1","gene_id":"TGGT1_249680","name":null,"product":"RNA polymerase II associated Paf1 complex component PAF1","uniprot_acc":null,"chromosome":"TGGT1_chrXII","start_pos":4664275},{"strain":"RH88","gene_id":"TGRH88_063420","name":null,"product":"RNA polymerase II associated Paf1 complex component PAF1","uniprot_acc":null,"chromosome":"CM023093","start_pos":4786188},{"strain":"VEG","gene_id":"TGVEG_249680","name":null,"product":"RNA polymerase II associated Paf1 complex component PAF1","uniprot_acc":"B6KHH8","chromosome":"TGVEG_chrXII","start_pos":4703491}]}