{"gene":"TG_313200","gene_symbol":"FBXL2","run_date":"2026-09-08T15:15:13","timeline":{"discoveries":[{"year":2024,"finding":"TgFBXL2 localizes to distinct perinucleolar sites within the nucleus of Toxoplasma gondii tachyzoites, as established by direct localization experiments.","method":"Subcellular localization (live imaging/fractionation implied by perinucleolar site description)","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization experiment reported in a peer-reviewed study; single lab but consistent with preprint version","pmids":["38814984"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"finding":"TgFBXL2 is stably engaged in an SCF-E3 ubiquitin ligase complex (SKP1–Cullin-1–F-box), identifying its role as an F-box protein that recruits substrates for poly-ubiquitination.","method":"Co-immunoprecipitation / biochemical complex isolation","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — stable complex engagement demonstrated in a peer-reviewed study, single lab, consistent with preprint","pmids":["38814984"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"finding":"The SCF-E3 complex containing TgFBXL2 is also associated with the COP9 signalosome, a complex known to negatively regulate SCF-E3 function, suggesting a regulatory brake on TgFBXL2-mediated ubiquitination activity.","method":"Co-immunoprecipitation / biochemical complex isolation","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — complex association established in a peer-reviewed study, single lab, replicated from preprint","pmids":["38814984"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"finding":"Conditional depletion of TgFBXL2 causes severe defects in centrosome replication and daughter cell development, establishing a role for TgFBXL2 in cell division.","method":"Conditional knockdown (auxin-inducible degron or similar) with phenotypic readout of centrosome and daughter cell morphology","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined cellular phenotype in peer-reviewed publication, single lab","pmids":["38814984"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"finding":"Conditional depletion of TgFBXL2 induces expression of stage-specific genes including a large cohort of genes necessary for sexual commitment (feline-restricted genes), demonstrating that TgFBXL2 functions as a repressor of sexual stage gene expression in tachyzoites.","method":"Conditional knockdown followed by RNAseq transcriptome profiling","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with genome-wide transcriptional readout, peer-reviewed publication replicated from preprint, two orthogonal methods (depletion + RNAseq)","pmids":["38814984"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"TgFBXL2 is a Toxoplasma gondii F-box protein that localizes to perinucleolar sites, forms a stable SCF-E3 ubiquitin ligase complex associated with the COP9 signalosome, and acts as a transcriptional repressor of sexual-stage (feline-restricted) genes in tachyzoites while also being required for centrosome replication and daughter cell development."},"narrative":{"mechanistic_narrative":"TgFBXL2 is a Toxoplasma gondii F-box protein that couples SCF-type ubiquitin ligase activity to the control of developmental gene expression and cell division [PMID:38814984]. It functions as the substrate-recognition subunit of a stably assembled SCF-E3 ubiquitin ligase complex (SKP1–Cullin-1–F-box) that recruits substrates for poly-ubiquitination, and this complex is further associated with the COP9 signalosome, a known negative regulator of SCF-E3 activity [PMID:38814984]. The protein concentrates at distinct perinucleolar sites within the tachyzoite nucleus [PMID:38814984]. Conditional depletion establishes two essential roles: TgFBXL2 represses sexual-stage (feline-restricted) gene programs in tachyzoites, since its loss de-represses a large cohort of sexual-commitment genes, and it is required for centrosome replication and daughter cell development [PMID:38814984]. The direct ubiquitination substrates through which TgFBXL2 exerts transcriptional repression and cell-division control have not been identified in the available corpus.","teleology":[{"year":2024,"claim":"Establishing where TgFBXL2 acts pinpointed a nuclear, perinucleolar site of function, framing it as a candidate regulator of nuclear/transcriptional processes rather than a cytoplasmic factor.","evidence":"Subcellular localization in T. gondii tachyzoites","pmids":["38814984"],"confidence":"Medium","gaps":["Localization does not define what TgFBXL2 does at perinucleolar sites","Mechanism of nuclear/perinucleolar targeting unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"claim":"Biochemical isolation showed TgFBXL2 is stably engaged in an SKP1–Cullin-1–F-box SCF complex, defining it as a substrate-recruiting subunit of an E3 ubiquitin ligase.","evidence":"Co-immunoprecipitation / biochemical complex isolation in T. gondii","pmids":["38814984"],"confidence":"Medium","gaps":["No ubiquitination substrate identified","Ligase activity not reconstituted in vitro"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"claim":"Detection of COP9 signalosome association with the TgFBXL2 SCF complex identified a potential regulatory brake on its ubiquitination activity.","evidence":"Co-immunoprecipitation / biochemical complex isolation in T. gondii","pmids":["38814984"],"confidence":"Medium","gaps":["Functional consequence of COP9 signalosome association not tested","Whether the signalosome activates or restrains TgFBXL2 in vivo unresolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"claim":"Conditional depletion revealed that TgFBXL2 is required for centrosome replication and daughter cell development, linking this F-box protein to the parasite cell-division machinery.","evidence":"Conditional knockdown with phenotypic readout of centrosome and daughter cell morphology in T. gondii","pmids":["38814984"],"confidence":"Medium","gaps":["Substrate driving the centrosome phenotype unknown","Whether the division defect is direct or secondary to transcriptional derepression not resolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"claim":"Depletion coupled to transcriptome profiling showed loss of TgFBXL2 de-represses sexual-stage (feline-restricted) genes, establishing it as a repressor of the sexual-commitment program in tachyzoites.","evidence":"Conditional knockdown followed by RNAseq transcriptome profiling in T. gondii","pmids":["38814984"],"confidence":"High","gaps":["Repression mechanism (direct ubiquitination of a transcription factor vs indirect) not defined","Ubiquitination substrate mediating repression unidentified"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"The direct poly-ubiquitination substrate(s) of the TgFBXL2 SCF complex, and how substrate turnover mechanistically links to sexual-stage gene repression and centrosome replication, remain unknown.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No substrate identified","No mechanistic link established between ubiquitination activity and the transcriptional or division phenotypes"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["SCF (SKP1–Cullin-1–F-box) E3 ubiquitin ligase complex","COP9 signalosome-associated SCF complex"],"partners":["SKP1","CULLIN-1","COP9 SIGNALOSOME"],"other_free_text":["Required for centrosome replication and daughter cell development in T. gondii tachyzoites","Represses sexual-stage (feline-restricted) gene expression in tachyzoites","Direct ubiquitination substrate(s) not identified in the available corpus"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"38814984","id":"PMC_38814984","title":"The Toxoplasma gondii F-Box Protein L2 Functions as a Repressor of Stage Specific Gene Expression.","date":"2024","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/38814984","citation_count":6,"is_preprint":false},{"pmid":"38187549","id":"PMC_38187549","title":"Toxoplasma gondii F-Box Protein L2 Silences Feline-Restricted Genes Necessary for Sexual Commitment.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38187549","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3641,"output_tokens":1185,"usd":0.014349,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6150,"output_tokens":2620,"usd":0.048125,"stage2_stop_reason":"end_turn"},"total_usd":0.062474,"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\": 2024,\n      \"finding\": \"TgFBXL2 localizes to distinct perinucleolar sites within the nucleus of Toxoplasma gondii tachyzoites, as established by direct localization experiments.\",\n      \"method\": \"Subcellular localization (live imaging/fractionation implied by perinucleolar site description)\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization experiment reported in a peer-reviewed study; single lab but consistent with preprint version\",\n      \"pmids\": [\"38814984\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TgFBXL2 is stably engaged in an SCF-E3 ubiquitin ligase complex (SKP1–Cullin-1–F-box), identifying its role as an F-box protein that recruits substrates for poly-ubiquitination.\",\n      \"method\": \"Co-immunoprecipitation / biochemical complex isolation\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — stable complex engagement demonstrated in a peer-reviewed study, single lab, consistent with preprint\",\n      \"pmids\": [\"38814984\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The SCF-E3 complex containing TgFBXL2 is also associated with the COP9 signalosome, a complex known to negatively regulate SCF-E3 function, suggesting a regulatory brake on TgFBXL2-mediated ubiquitination activity.\",\n      \"method\": \"Co-immunoprecipitation / biochemical complex isolation\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — complex association established in a peer-reviewed study, single lab, replicated from preprint\",\n      \"pmids\": [\"38814984\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Conditional depletion of TgFBXL2 causes severe defects in centrosome replication and daughter cell development, establishing a role for TgFBXL2 in cell division.\",\n      \"method\": \"Conditional knockdown (auxin-inducible degron or similar) with phenotypic readout of centrosome and daughter cell morphology\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined cellular phenotype in peer-reviewed publication, single lab\",\n      \"pmids\": [\"38814984\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Conditional depletion of TgFBXL2 induces expression of stage-specific genes including a large cohort of genes necessary for sexual commitment (feline-restricted genes), demonstrating that TgFBXL2 functions as a repressor of sexual stage gene expression in tachyzoites.\",\n      \"method\": \"Conditional knockdown followed by RNAseq transcriptome profiling\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with genome-wide transcriptional readout, peer-reviewed publication replicated from preprint, two orthogonal methods (depletion + RNAseq)\",\n      \"pmids\": [\"38814984\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"TgFBXL2 is a Toxoplasma gondii F-box protein that localizes to perinucleolar sites, forms a stable SCF-E3 ubiquitin ligase complex associated with the COP9 signalosome, and acts as a transcriptional repressor of sexual-stage (feline-restricted) genes in tachyzoites while also being required for centrosome replication and daughter cell development.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TgFBXL2 is a Toxoplasma gondii F-box protein that couples SCF-type ubiquitin ligase activity to the control of developmental gene expression and cell division [#1, #4]. It functions as the substrate-recognition subunit of a stably assembled SCF-E3 ubiquitin ligase complex (SKP1\\u2013Cullin-1\\u2013F-box) that recruits substrates for poly-ubiquitination, and this complex is further associated with the COP9 signalosome, a known negative regulator of SCF-E3 activity [#1, #2]. The protein concentrates at distinct perinucleolar sites within the tachyzoite nucleus [#0]. Conditional depletion establishes two essential roles: TgFBXL2 represses sexual-stage (feline-restricted) gene programs in tachyzoites, since its loss de-represses a large cohort of sexual-commitment genes, and it is required for centrosome replication and daughter cell development [#3, #4]. The direct ubiquitination substrates through which TgFBXL2 exerts transcriptional repression and cell-division control have not been identified in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2024,\n      \"claim\": \"Establishing where TgFBXL2 acts pinpointed a nuclear, perinucleolar site of function, framing it as a candidate regulator of nuclear/transcriptional processes rather than a cytoplasmic factor.\",\n      \"evidence\": \"Subcellular localization in T. gondii tachyzoites\",\n      \"pmids\": [\"38814984\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Localization does not define what TgFBXL2 does at perinucleolar sites\", \"Mechanism of nuclear/perinucleolar targeting unknown\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Biochemical isolation showed TgFBXL2 is stably engaged in an SKP1\\u2013Cullin-1\\u2013F-box SCF complex, defining it as a substrate-recruiting subunit of an E3 ubiquitin ligase.\",\n      \"evidence\": \"Co-immunoprecipitation / biochemical complex isolation in T. gondii\",\n      \"pmids\": [\"38814984\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No ubiquitination substrate identified\", \"Ligase activity not reconstituted in vitro\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Detection of COP9 signalosome association with the TgFBXL2 SCF complex identified a potential regulatory brake on its ubiquitination activity.\",\n      \"evidence\": \"Co-immunoprecipitation / biochemical complex isolation in T. gondii\",\n      \"pmids\": [\"38814984\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of COP9 signalosome association not tested\", \"Whether the signalosome activates or restrains TgFBXL2 in vivo unresolved\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Conditional depletion revealed that TgFBXL2 is required for centrosome replication and daughter cell development, linking this F-box protein to the parasite cell-division machinery.\",\n      \"evidence\": \"Conditional knockdown with phenotypic readout of centrosome and daughter cell morphology in T. gondii\",\n      \"pmids\": [\"38814984\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Substrate driving the centrosome phenotype unknown\", \"Whether the division defect is direct or secondary to transcriptional derepression not resolved\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Depletion coupled to transcriptome profiling showed loss of TgFBXL2 de-represses sexual-stage (feline-restricted) genes, establishing it as a repressor of the sexual-commitment program in tachyzoites.\",\n      \"evidence\": \"Conditional knockdown followed by RNAseq transcriptome profiling in T. gondii\",\n      \"pmids\": [\"38814984\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Repression mechanism (direct ubiquitination of a transcription factor vs indirect) not defined\", \"Ubiquitination substrate mediating repression unidentified\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct poly-ubiquitination substrate(s) of the TgFBXL2 SCF complex, and how substrate turnover mechanistically links to sexual-stage gene repression and centrosome replication, remain unknown.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No substrate identified\", \"No mechanistic link established between ubiquitination activity and the transcriptional or division phenotypes\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0061630\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:1990756\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0003714\", \"supporting_discovery_ids\": [4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0016567\", \"supporting_discovery_ids\": [1, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0051726\", \"supporting_discovery_ids\": [3], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0010468\", \"supporting_discovery_ids\": [4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\n      \"SCF (SKP1\\u2013Cullin-1\\u2013F-box) E3 ubiquitin ligase complex\",\n      \"COP9 signalosome-associated SCF complex\"\n    ],\n    \"partners\": [\n      \"SKP1\",\n      \"Cullin-1\",\n      \"COP9 signalosome\"\n    ],\n    \"other_free_text\": [\n      \"Required for centrosome replication and daughter cell development in T. gondii tachyzoites\",\n      \"Represses sexual-stage (feline-restricted) gene expression in tachyzoites\",\n      \"Direct ubiquitination substrate(s) not identified in the available corpus\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_313200","name":"FBXL2","product":"F-Box Protein L2","uniprot_acc":"S8EUA4","chromosome":"TGME49_chrXI","start_pos":3168508},{"strain":"GT1","gene_id":"TGGT1_313200","name":null,"product":"leucine rich repeat-containing protein","uniprot_acc":null,"chromosome":"TGGT1_chrXI","start_pos":3132254},{"strain":"RH88","gene_id":"TGRH88_052330","name":null,"product":"leucine rich repeat-containing protein","uniprot_acc":null,"chromosome":"CM023092","start_pos":3217966},{"strain":"VEG","gene_id":"TGVEG_313200","name":null,"product":"leucine rich repeat-containing protein","uniprot_acc":"A0A125YUX1","chromosome":"TGVEG_chrXI","start_pos":3181352}]}