{"gene":"TG_223125","gene_symbol":"PUBL","run_date":"2026-09-08T11:06:40","timeline":{"discoveries":[{"year":2017,"finding":"PUBL (plastid ubiquitin-like protein) is an apicoplast-localized protein derived from a ubiquitin ancestor that functions in protein import across the periplastid membrane of the apicoplast in Toxoplasma gondii.","method":"Conditional null mutants and genetic complementation assays demonstrating loss of apicoplast protein import and parasite lethality upon PUBL depletion.","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional null mutants, genetic complementation, and epistasis with CDC48AP using established functional import assays in a single rigorous study.","pmids":["28655825"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"finding":"PUBL acts together with the AAA ATPase CDC48AP to translocate apicoplast proteins across the periplastid membrane, functioning within an apicoplast-specific ERAD-like complex.","method":"Genetic epistasis analysis using conditional null mutants of PUBL and CDC48AP, with apicoplast protein import assays.","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 / Strong — epistasis established by double conditional null mutants with a defined functional readout (protein translocation across periplastid membrane), single rigorous study with multiple genetic tools.","pmids":["28655825"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"finding":"PUBL residues homologous to those required for ubiquitin conjugation onto target proteins are essential for its function in apicoplast protein import, whereas residues required for polyubiquitination and preprotein processing are dispensable.","method":"Site-directed mutagenesis of PUBL residues homologous to ubiquitin conjugation sites, followed by genetic complementation and apicoplast protein import assays.","journal":"mBio","confidence":"High","confidence_rationale":"Tier 1 / Moderate — active-site mutagenesis with functional complementation assay, single lab but multiple mutants tested with clear mechanistic resolution.","pmids":["28655825"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"PUBL is a divergent, apicoplast-localized ubiquitin-like protein that cooperates with the AAA ATPase CDC48AP within an apicoplast-specific ERAD-like machinery to drive protein translocation across the periplastid membrane; its ubiquitin-conjugation-homologous residues are essential for this activity, while polyubiquitination and preprotein-processing residues are dispensable, and loss of PUBL is lethal to the parasite."},"narrative":{"mechanistic_narrative":"PUBL (plastid ubiquitin-like protein) is a divergent, ubiquitin-derived protein that drives the import of nucleus-encoded proteins across the periplastid membrane of the apicoplast in Toxoplasma gondii, an activity essential for parasite viability [PMID:28655825]. It operates within an apicoplast-specific ERAD-like machinery together with the AAA ATPase CDC48AP, with which it acts epistatically to translocate apicoplast proteins across the periplastid membrane [PMID:28655825]. Mechanistically, the residues of PUBL homologous to those required for ubiquitin conjugation onto target proteins are essential for import, whereas residues homologous to polyubiquitination and preprotein-processing determinants are dispensable, indicating that a conjugation-like chemistry rather than canonical polyubiquitin signaling underlies its translocation function [PMID:28655825]. Beyond these findings, no further mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2017,"claim":"Whether a ubiquitin-derived protein contributes to apicoplast biogenesis was unknown; identifying PUBL as an apicoplast-localized, ubiquitin-ancestor-derived protein essential for protein import across the periplastid membrane established a dedicated import factor whose loss is lethal.","evidence":"Conditional null mutants and genetic complementation with apicoplast protein import assays in Toxoplasma gondii","pmids":["28655825"],"confidence":"High","gaps":["Direct biochemical demonstration of PUBL conjugation to a substrate not shown","Substrate identity of imported proteins not defined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"claim":"How PUBL couples to the translocation machinery was unresolved; epistasis with the AAA ATPase CDC48AP placed PUBL within an apicoplast-specific ERAD-like complex that drives translocation across the periplastid membrane.","evidence":"Genetic epistasis using double conditional null mutants of PUBL and CDC48AP with a periplastid-membrane translocation readout in Toxoplasma gondii","pmids":["28655825"],"confidence":"High","gaps":["Physical composition and stoichiometry of the ERAD-like complex not resolved","Mechanism by which CDC48AP extracts PUBL-marked substrates not shown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"claim":"Which biochemical features of PUBL matter for import was unknown; mutagenesis showed that conjugation-homologous residues are essential while polyubiquitination- and preprotein-processing-homologous residues are dispensable, defining a conjugation-like rather than canonical ubiquitin-signaling mechanism.","evidence":"Site-directed mutagenesis of ubiquitin-homologous residues with genetic complementation and import assays in Toxoplasma gondii","pmids":["28655825"],"confidence":"High","gaps":["The specific conjugation target of PUBL not identified","Enzymes activating/conjugating PUBL not characterized"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"The direct molecular substrate(s) of PUBL conjugation and the full enzymatic cascade (activating/conjugating machinery) that couple PUBL modification to CDC48AP-driven translocation remain undefined.","evidence":"","pmids":[],"confidence":"High","gaps":["No conjugation substrate identified","Activating/conjugating enzymes for PUBL unknown","Structural basis of PUBL function not determined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Apicoplast-specific ERAD-like translocation complex (with CDC48AP)"],"partners":["CDC48AP"],"other_free_text":["PUBL is derived from a ubiquitin ancestor; conjugation-homologous residues are essential for import while polyubiquitination and preprotein-processing residues are dispensable [#2].","PUBL depletion abolishes apicoplast protein import and is lethal to Toxoplasma gondii [#0]."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"28655825","id":"PMC_28655825","title":"A Plastid Protein That Evolved from Ubiquitin and Is Required for Apicoplast Protein Import in Toxoplasma gondii.","date":"2017","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/28655825","citation_count":28,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3207,"output_tokens":819,"usd":0.010953,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5618,"output_tokens":1986,"usd":0.03887,"stage2_stop_reason":"end_turn"},"total_usd":0.049823,"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\": 2017,\n      \"finding\": \"PUBL (plastid ubiquitin-like protein) is an apicoplast-localized protein derived from a ubiquitin ancestor that functions in protein import across the periplastid membrane of the apicoplast in Toxoplasma gondii.\",\n      \"method\": \"Conditional null mutants and genetic complementation assays demonstrating loss of apicoplast protein import and parasite lethality upon PUBL depletion.\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional null mutants, genetic complementation, and epistasis with CDC48AP using established functional import assays in a single rigorous study.\",\n      \"pmids\": [\"28655825\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"PUBL acts together with the AAA ATPase CDC48AP to translocate apicoplast proteins across the periplastid membrane, functioning within an apicoplast-specific ERAD-like complex.\",\n      \"method\": \"Genetic epistasis analysis using conditional null mutants of PUBL and CDC48AP, with apicoplast protein import assays.\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — epistasis established by double conditional null mutants with a defined functional readout (protein translocation across periplastid membrane), single rigorous study with multiple genetic tools.\",\n      \"pmids\": [\"28655825\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"PUBL residues homologous to those required for ubiquitin conjugation onto target proteins are essential for its function in apicoplast protein import, whereas residues required for polyubiquitination and preprotein processing are dispensable.\",\n      \"method\": \"Site-directed mutagenesis of PUBL residues homologous to ubiquitin conjugation sites, followed by genetic complementation and apicoplast protein import assays.\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — active-site mutagenesis with functional complementation assay, single lab but multiple mutants tested with clear mechanistic resolution.\",\n      \"pmids\": [\"28655825\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PUBL is a divergent, apicoplast-localized ubiquitin-like protein that cooperates with the AAA ATPase CDC48AP within an apicoplast-specific ERAD-like machinery to drive protein translocation across the periplastid membrane; its ubiquitin-conjugation-homologous residues are essential for this activity, while polyubiquitination and preprotein-processing residues are dispensable, and loss of PUBL is lethal to the parasite.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PUBL (plastid ubiquitin-like protein) is a divergent, ubiquitin-derived protein that drives the import of nucleus-encoded proteins across the periplastid membrane of the apicoplast in Toxoplasma gondii, an activity essential for parasite viability [#0]. It operates within an apicoplast-specific ERAD-like machinery together with the AAA ATPase CDC48AP, with which it acts epistatically to translocate apicoplast proteins across the periplastid membrane [#1]. Mechanistically, the residues of PUBL homologous to those required for ubiquitin conjugation onto target proteins are essential for import, whereas residues homologous to polyubiquitination and preprotein-processing determinants are dispensable, indicating that a conjugation-like chemistry rather than canonical polyubiquitin signaling underlies its translocation function [#2]. Beyond these findings, no further mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Whether a ubiquitin-derived protein contributes to apicoplast biogenesis was unknown; identifying PUBL as an apicoplast-localized, ubiquitin-ancestor-derived protein essential for protein import across the periplastid membrane established a dedicated import factor whose loss is lethal.\",\n      \"evidence\": \"Conditional null mutants and genetic complementation with apicoplast protein import assays in Toxoplasma gondii\",\n      \"pmids\": [\"28655825\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct biochemical demonstration of PUBL conjugation to a substrate not shown\", \"Substrate identity of imported proteins not defined\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"How PUBL couples to the translocation machinery was unresolved; epistasis with the AAA ATPase CDC48AP placed PUBL within an apicoplast-specific ERAD-like complex that drives translocation across the periplastid membrane.\",\n      \"evidence\": \"Genetic epistasis using double conditional null mutants of PUBL and CDC48AP with a periplastid-membrane translocation readout in Toxoplasma gondii\",\n      \"pmids\": [\"28655825\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physical composition and stoichiometry of the ERAD-like complex not resolved\", \"Mechanism by which CDC48AP extracts PUBL-marked substrates not shown\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Which biochemical features of PUBL matter for import was unknown; mutagenesis showed that conjugation-homologous residues are essential while polyubiquitination- and preprotein-processing-homologous residues are dispensable, defining a conjugation-like rather than canonical ubiquitin-signaling mechanism.\",\n      \"evidence\": \"Site-directed mutagenesis of ubiquitin-homologous residues with genetic complementation and import assays in Toxoplasma gondii\",\n      \"pmids\": [\"28655825\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The specific conjugation target of PUBL not identified\", \"Enzymes activating/conjugating PUBL not characterized\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct molecular substrate(s) of PUBL conjugation and the full enzymatic cascade (activating/conjugating machinery) that couple PUBL modification to CDC48AP-driven translocation remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No conjugation substrate identified\", \"Activating/conjugating enzymes for PUBL unknown\", \"Structural basis of PUBL function not determined\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0031386\", \"supporting_discovery_ids\": [0, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0065002\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0009507\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0045037\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0036503\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"Apicoplast-specific ERAD-like translocation complex (with CDC48AP)\"],\n    \"partners\": [\"CDC48AP\"],\n    \"other_free_text\": [\n      \"PUBL is derived from a ubiquitin ancestor; conjugation-homologous residues are essential for import while polyubiquitination and preprotein-processing residues are dispensable [#2].\",\n      \"PUBL depletion abolishes apicoplast protein import and is lethal to Toxoplasma gondii [#0].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_223125","name":"PUBL","product":"plastid ubiquitin-like protein PUBL","uniprot_acc":"S8F891","chromosome":"TGME49_chrII","start_pos":1458334},{"strain":"GT1","gene_id":"TGGT1_223125","name":null,"product":"ubiquitin family protein","uniprot_acc":null,"chromosome":"TGGT1_chrII","start_pos":1441069},{"strain":"RH88","gene_id":"TGRH88_001840","name":null,"product":"ubiquitin family protein","uniprot_acc":null,"chromosome":"CM023083","start_pos":1614789},{"strain":"VEG","gene_id":"TGVEG_223125","name":null,"product":"ubiquitin family protein","uniprot_acc":"A0A125YL99","chromosome":"TGVEG_chrII","start_pos":1464773}]}