{"gene":"TG_212100","gene_symbol":"UBA1","run_date":"2026-09-08T11:06:24","timeline":{"discoveries":[{"year":2022,"finding":"TgUba1 is localized to the cytoplasm of Toxoplasma gondii, as determined by direct localization experiments.","method":"Subcellular localization experiment (direct imaging/fractionation)","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single lab, localization reported without detailed functional consequence linked specifically to cytoplasmic localization","pmids":["36142209"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"TgUba1 physically interacts with TgUrm1 (ubiquitin-related Modifier 1), and the E1-like domain (AD domain) of TgUba1 is essential for this interaction.","method":"Protein interaction assay (pulldown/co-immunoprecipitation) with domain-deletion mapping","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — interaction demonstrated with domain-level mapping in a single lab, two orthogonal lines of evidence (interaction assay + domain mutant)","pmids":["36142209"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"Knockout of TgUba1 (via CRISPR/Cas9) attenuates parasite proliferation and virulence in mice, but does not affect invasion or egress, establishing TgUba1 as essential for T. gondii survival and replication.","method":"CRISPR/Cas9 knockout with complementation, in vitro proliferation assays, and in vivo virulence assay in mice","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with complementation and defined cellular/in vivo phenotype, single lab","pmids":["36142209"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"In the absence of TgUba1, the TgUrm1 conjugate band is significantly reduced under oxidative stress (diamide stimulation), indicating that TgUba1 enhances the targeted conjugation (urmylation) ability of TgUrm1 in response to oxidative stress.","method":"Western blot analysis of TgUrm1 conjugates in TgUba1 knockout parasites under oxidative stress conditions","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO with defined biochemical readout (conjugate band reduction) under specific stress condition, single lab","pmids":["36142209"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"Eleven TgUba1-interacting proteins were identified by proximity-based protein labeling (BioID-type), linking TgUba1 to ubiquitin-like modifications, anti-oxidative stress, and metabolic regulation processes.","method":"Proximity-based protein labeling (BioID/proximity ligation) followed by mass spectrometry","journal":"International journal of molecular sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — proximity labeling identifies candidate interactors without further validation of individual interactions in this abstract","pmids":["36142209"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"TgUba1 is a cytoplasmic E1-like ubiquitin-activating enzyme in Toxoplasma gondii that physically interacts with TgUrm1 via its AD (E1-like) domain, promotes TgUrm1 conjugation to target proteins under oxidative stress (particularly diamide), and is essential for parasite proliferation and virulence in mice but dispensable for invasion and egress."},"narrative":{"mechanistic_narrative":"TgUba1 is a cytoplasmic E1-like ubiquitin-activating enzyme in Toxoplasma gondii that functions in the ubiquitin-like modification pathway centered on the modifier TgUrm1 [PMID:36142209]. It physically interacts with TgUrm1 through its E1-like AD domain, which is required for the interaction [PMID:36142209], and it promotes TgUrm1 conjugation (urmylation) of target proteins specifically under oxidative stress, since loss of TgUba1 sharply reduces TgUrm1 conjugate formation upon diamide challenge [PMID:36142209]. Genetically, TgUba1 is essential for parasite proliferation and for virulence in mice but is dispensable for host-cell invasion and egress [PMID:36142209]. Proximity-based interaction mapping links TgUba1 to ubiquitin-like modification, anti-oxidative stress, and metabolic regulation processes [PMID:36142209]. Beyond these findings, no further mechanistic detail — including direct catalytic characterization or defined urmylation substrates — has been characterized in the available corpus.","teleology":[{"year":2022,"claim":"Establishing where TgUba1 acts in the cell provided the first spatial context for its role in an activating-enzyme pathway.","evidence":"Subcellular localization experiment in T. gondii","pmids":["36142209"],"confidence":"Medium","gaps":["No functional consequence tied specifically to cytoplasmic localization","No information on dynamic relocalization under stress"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"Whether TgUba1 engages the ubiquitin-like modifier TgUrm1 and through which domain was resolved, defining it as the activating partner in an Urm1 conjugation system.","evidence":"Pulldown/co-IP with AD (E1-like) domain-deletion mapping in T. gondii","pmids":["36142209"],"confidence":"Medium","gaps":["Direct catalytic (thioester/adenylation) activity toward TgUrm1 not demonstrated","Reciprocal or in vitro reconstitution of the interaction not shown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"The physiological output of TgUba1 was defined by showing it is required for TgUrm1 conjugation specifically under oxidative stress, connecting the enzyme to a stress-responsive modification.","evidence":"Western blot of TgUrm1 conjugate band in TgUba1 knockout parasites under diamide stimulation","pmids":["36142209"],"confidence":"Medium","gaps":["Urmylation substrate proteins not identified","Biochemical mechanism of stress-triggered enhancement unresolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"The importance of TgUba1 for the parasite lifecycle was established by genetic ablation, distinguishing which processes depend on it.","evidence":"CRISPR/Cas9 knockout with complementation, in vitro proliferation assays, and mouse virulence assay","pmids":["36142209"],"confidence":"Medium","gaps":["Molecular basis linking loss of urmylation to the proliferation/virulence defect not established","No mechanistic explanation for why invasion and egress are unaffected"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"A candidate interactome was generated to place TgUba1 within broader cellular processes.","evidence":"Proximity-based (BioID-type) labeling with mass spectrometry in T. gondii","pmids":["36142209"],"confidence":"Low","gaps":["Individual interactors not independently validated","Functional relevance of the identified proteins to TgUba1 activity untested"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"The direct enzymatic mechanism of TgUba1 and the identity of urmylated substrates driving proliferation and virulence remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No in vitro reconstitution of TgUrm1 activation/conjugation","No defined urmylation substrate set","Causal link between urmylation loss and virulence attenuation undefined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["TGURM1 (UBIQUITIN-RELATED MODIFIER 1) — PHYSICAL INTERACTOR VIA TGUBA1 AD/E1-LIKE DOMAIN [#1]"],"other_free_text":["Essential for T. gondii proliferation and mouse virulence but dispensable for invasion and egress [#2]","Promotes TgUrm1 conjugation (urmylation) specifically under oxidative (diamide) stress [#3]","Eleven candidate proximity interactors link TgUba1 to ubiquitin-like modification, anti-oxidative stress, and metabolic regulation [#4]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"36142209","id":"PMC_36142209","title":"Uba1: A Potential Ubiquitin-like Activator Protein of Urm1 in Toxoplasma gondii.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36142209","citation_count":4,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3000,"output_tokens":1174,"usd":0.013305,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6164,"output_tokens":2313,"usd":0.044323,"stage2_stop_reason":"end_turn"},"total_usd":0.057628,"stage1_batch_id":"msgbatch_01WokvBYTB6JLnYrpD4rXnyV","stage2_batch_id":"msgbatch_01M7hsQDvz6AqVC9DLVjQzzc","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2022,\n      \"finding\": \"TgUba1 is localized to the cytoplasm of Toxoplasma gondii, as determined by direct localization experiments.\",\n      \"method\": \"Subcellular localization experiment (direct imaging/fractionation)\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, localization reported without detailed functional consequence linked specifically to cytoplasmic localization\",\n      \"pmids\": [\"36142209\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TgUba1 physically interacts with TgUrm1 (ubiquitin-related Modifier 1), and the E1-like domain (AD domain) of TgUba1 is essential for this interaction.\",\n      \"method\": \"Protein interaction assay (pulldown/co-immunoprecipitation) with domain-deletion mapping\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — interaction demonstrated with domain-level mapping in a single lab, two orthogonal lines of evidence (interaction assay + domain mutant)\",\n      \"pmids\": [\"36142209\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Knockout of TgUba1 (via CRISPR/Cas9) attenuates parasite proliferation and virulence in mice, but does not affect invasion or egress, establishing TgUba1 as essential for T. gondii survival and replication.\",\n      \"method\": \"CRISPR/Cas9 knockout with complementation, in vitro proliferation assays, and in vivo virulence assay in mice\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with complementation and defined cellular/in vivo phenotype, single lab\",\n      \"pmids\": [\"36142209\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In the absence of TgUba1, the TgUrm1 conjugate band is significantly reduced under oxidative stress (diamide stimulation), indicating that TgUba1 enhances the targeted conjugation (urmylation) ability of TgUrm1 in response to oxidative stress.\",\n      \"method\": \"Western blot analysis of TgUrm1 conjugates in TgUba1 knockout parasites under oxidative stress conditions\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO with defined biochemical readout (conjugate band reduction) under specific stress condition, single lab\",\n      \"pmids\": [\"36142209\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Eleven TgUba1-interacting proteins were identified by proximity-based protein labeling (BioID-type), linking TgUba1 to ubiquitin-like modifications, anti-oxidative stress, and metabolic regulation processes.\",\n      \"method\": \"Proximity-based protein labeling (BioID/proximity ligation) followed by mass spectrometry\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — proximity labeling identifies candidate interactors without further validation of individual interactions in this abstract\",\n      \"pmids\": [\"36142209\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"TgUba1 is a cytoplasmic E1-like ubiquitin-activating enzyme in Toxoplasma gondii that physically interacts with TgUrm1 via its AD (E1-like) domain, promotes TgUrm1 conjugation to target proteins under oxidative stress (particularly diamide), and is essential for parasite proliferation and virulence in mice but dispensable for invasion and egress.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TgUba1 is a cytoplasmic E1-like ubiquitin-activating enzyme in Toxoplasma gondii that functions in the ubiquitin-like modification pathway centered on the modifier TgUrm1 [#0, #1]. It physically interacts with TgUrm1 through its E1-like AD domain, which is required for the interaction [#1], and it promotes TgUrm1 conjugation (urmylation) of target proteins specifically under oxidative stress, since loss of TgUba1 sharply reduces TgUrm1 conjugate formation upon diamide challenge [#3]. Genetically, TgUba1 is essential for parasite proliferation and for virulence in mice but is dispensable for host-cell invasion and egress [#2]. Proximity-based interaction mapping links TgUba1 to ubiquitin-like modification, anti-oxidative stress, and metabolic regulation processes [#4]. Beyond these findings, no further mechanistic detail — including direct catalytic characterization or defined urmylation substrates — has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Establishing where TgUba1 acts in the cell provided the first spatial context for its role in an activating-enzyme pathway.\",\n      \"evidence\": \"Subcellular localization experiment in T. gondii\",\n      \"pmids\": [\"36142209\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional consequence tied specifically to cytoplasmic localization\",\n        \"No information on dynamic relocalization under stress\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Whether TgUba1 engages the ubiquitin-like modifier TgUrm1 and through which domain was resolved, defining it as the activating partner in an Urm1 conjugation system.\",\n      \"evidence\": \"Pulldown/co-IP with AD (E1-like) domain-deletion mapping in T. gondii\",\n      \"pmids\": [\"36142209\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct catalytic (thioester/adenylation) activity toward TgUrm1 not demonstrated\",\n        \"Reciprocal or in vitro reconstitution of the interaction not shown\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"The physiological output of TgUba1 was defined by showing it is required for TgUrm1 conjugation specifically under oxidative stress, connecting the enzyme to a stress-responsive modification.\",\n      \"evidence\": \"Western blot of TgUrm1 conjugate band in TgUba1 knockout parasites under diamide stimulation\",\n      \"pmids\": [\"36142209\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Urmylation substrate proteins not identified\",\n        \"Biochemical mechanism of stress-triggered enhancement unresolved\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"The importance of TgUba1 for the parasite lifecycle was established by genetic ablation, distinguishing which processes depend on it.\",\n      \"evidence\": \"CRISPR/Cas9 knockout with complementation, in vitro proliferation assays, and mouse virulence assay\",\n      \"pmids\": [\"36142209\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Molecular basis linking loss of urmylation to the proliferation/virulence defect not established\",\n        \"No mechanistic explanation for why invasion and egress are unaffected\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"A candidate interactome was generated to place TgUba1 within broader cellular processes.\",\n      \"evidence\": \"Proximity-based (BioID-type) labeling with mass spectrometry in T. gondii\",\n      \"pmids\": [\"36142209\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Individual interactors not independently validated\",\n        \"Functional relevance of the identified proteins to TgUba1 activity untested\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct enzymatic mechanism of TgUba1 and the identity of urmylated substrates driving proliferation and virulence remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No in vitro reconstitution of TgUrm1 activation/conjugation\",\n        \"No defined urmylation substrate set\",\n        \"Causal link between urmylation loss and virulence attenuation undefined\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008641\", \"supporting_discovery_ids\": [1, 3], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005737\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0032447\", \"supporting_discovery_ids\": [1, 3], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0006979\", \"supporting_discovery_ids\": [3, 4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"TgUrm1 (ubiquitin-related Modifier 1) — physical interactor via TgUba1 AD/E1-like domain [#1]\"\n    ],\n    \"other_free_text\": [\n      \"Essential for T. gondii proliferation and mouse virulence but dispensable for invasion and egress [#2]\",\n      \"Promotes TgUrm1 conjugation (urmylation) specifically under oxidative (diamide) stress [#3]\",\n      \"Eleven candidate proximity interactors link TgUba1 to ubiquitin-like modification, anti-oxidative stress, and metabolic regulation [#4]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_212100","name":"UBA1","product":"ubiquitin activating enzyme UBA1","uniprot_acc":"S8ETX6","chromosome":"TGME49_chrX","start_pos":4062568},{"strain":"GT1","gene_id":"TGGT1_212100","name":null,"product":"ThiF family protein","uniprot_acc":null,"chromosome":"TGGT1_chrX","start_pos":3968778},{"strain":"RH88","gene_id":"TGRH88_042850","name":null,"product":"ThiF family protein","uniprot_acc":null,"chromosome":"CM023091","start_pos":3480972},{"strain":"VEG","gene_id":"TGVEG_212100","name":null,"product":"ThiF family protein","uniprot_acc":"B9Q6W0","chromosome":"TGVEG_chrX","start_pos":3973447}]}