{"gene":"PF3D7_0923100","run_date":"2026-09-08T12:51:27","timeline":{"discoveries":[{"year":2017,"finding":"PfOTU (PF3D7_0923100) localizes to vesicular compartments and associates with the apicoplast, as shown by C-terminal regulatable fluorescent affinity tagging of the native protein in P. falciparum.","method":"Regulatable fluorescent affinity tag on native protein; live imaging/subcellular localization","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with functional consequence (apicoplast association), single lab, multiple orthogonal approaches (tagging, knockdown, rescue)","pmids":["28423214"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2017,"finding":"Knockdown of PfOTU by degradation-tag-mediated depletion causes abnormal apicoplast development, blocks parasite development beyond early-schizont stage, and impairs apicoplast protein import, establishing PfOTU as essential for apicoplast homeostasis.","method":"Degradation-tag-mediated knockdown; phenotypic analysis of apicoplast development and protein import; isoprenoid precursor rescue experiment","journal":"Cellular microbiology","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with defined cellular phenotype, isoprenoid rescue confirms apicoplast-specific role, multiple orthogonal readouts in single study","pmids":["28423214"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2017,"finding":"PfOTU is implicated in membrane deconjugation (delipidation) of Atg8, potentially linked to apicoplast protein import, suggesting a noncanonical role for Atg8 deconjugation in apicoplast maintenance.","method":"Functional characterization via knockdown and Atg8 deconjugation assay (biochemical evidence for membrane deconjugation activity)","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — single lab, multiple methods (knockdown + Atg8 deconjugation evidence), but described as 'possible biological function' indicating partial mechanistic follow-up","pmids":["28423214"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"finding":"The Plasmodium berghei ortholog of OTU (Otu) localizes to the apicoplast; genetic disruption of Otu individually is possible, but simultaneous deletion of Otu and Atg4 is refractory, indicating synthetic lethality and overlapping essential functions in Atg8 deconjugation.","method":"Gene knockout (individual and simultaneous); live localization; in vivo and in vitro Atg8 deconjugation analysis","journal":"Cellular and molecular life sciences : CMLS","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis (double KO refractory), confirmed localization, single lab, multiple orthogonal methods","pmids":["37910326"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2023,"finding":"Otu KO parasites in P. berghei show no visible developmental defects in blood or mosquito stages, and all Otu KO sporozoites establish blood-stage infection normally, indicating Otu is dispensable individually for these lifecycle stages. In contrast, Otu cleaves the peptide bond on the N-terminal side of glycine on Atg8, thereby irreversibly inactivating Atg8 rather than recycling it, distinguishing its mechanism from Atg4.","method":"Gene knockout; in vivo mouse infection assay; in vitro Atg8 deconjugation/cleavage site analysis","journal":"Cellular and molecular life sciences : CMLS","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO with defined phenotypic readout and biochemical mechanistic distinction (cleavage site), single lab","pmids":["37910326"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2021,"finding":"P. falciparum OTU-like protein (PF3D7_0923100) demonstrates ubiquitin and ISG15 deconjugation activities in vitro, as measured by intracellular ubiquitinated protein content via western blot and flow cytometry, and its enzymatic activity can be inhibited by small molecules with IC50 values as low as 30 nM.","method":"Deconjugation assay; structural modeling; small molecule inhibitor screening; enzyme kinetics; western blot and flow cytometry for ubiquitinated proteins","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro deconjugation assay establishing enzymatic activity, but single lab and limited mechanistic follow-up; structural model is computational","pmids":["34486667"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""},{"species":"Plasmodium vivax","strain":""},{"species":"Plasmodium yoelii","strain":""}]}],"current_model":"PF3D7_0923100 (PfOTU) is an OTU-domain cysteine protease that localizes to vesicular compartments and the apicoplast in P. falciparum, where it is essential for apicoplast homeostasis and protein import; it deconjugates Atg8 from membranes (and also ubiquitin/ISG15 substrates) by cleaving on the N-terminal side of the terminal glycine, thereby irreversibly inactivating Atg8 rather than recycling it, and it acts redundantly with Atg4 such that simultaneous loss of both is lethal to the parasite."},"narrative":{"mechanistic_narrative":"PF3D7_0923100 (PfOTU) is an OTU-domain cysteine deconjugating protease essential for apicoplast homeostasis in Plasmodium falciparum [PMID:28423214]. The native protein localizes to vesicular compartments and associates with the apicoplast [PMID:28423214], and its depletion causes abnormal apicoplast development, arrests parasites beyond the early-schizont stage, and impairs apicoplast protein import — a defect consistent with an apicoplast-specific role, as indicated by isoprenoid precursor rescue [PMID:28423214]. Mechanistically, PfOTU deconjugates (delipidates) Atg8 from membranes, a noncanonical activity linked to apicoplast maintenance [PMID:28423214], and in vitro it also cleaves ubiquitin and ISG15 conjugates, an activity blockable by small-molecule inhibitors with IC50 values as low as 30 nM [PMID:34486667]. Work on the P. berghei ortholog shows apicoplast localization and demonstrates that Otu cleaves the peptide bond on the N-terminal side of the terminal glycine of Atg8, irreversibly inactivating Atg8 rather than recycling it, thereby distinguishing its mechanism from Atg4; individual Otu deletion is tolerated with no visible blood- or mosquito-stage defect, but simultaneous deletion of Otu and Atg4 is refractory, revealing synthetic lethality and overlapping essential functions in Atg8 deconjugation [PMID:37910326].","teleology":[{"year":2017,"claim":"Establishing where PfOTU acts was the first requirement for assigning it a cellular role, and native tagging placed it at vesicular compartments and the apicoplast.","evidence":"Regulatable fluorescent affinity tag on native protein with live imaging in P. falciparum","pmids":["28423214"],"confidence":"Medium","gaps":["Single-lab localization; does not resolve whether apicoplast association is direct or via membrane trafficking","Does not define the enzymatic activity operating at this site"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2017,"claim":"Whether PfOTU is functionally important was answered by depletion, which showed it is essential for apicoplast development and protein import.","evidence":"Degradation-tag knockdown with apicoplast phenotyping, protein-import readout, and isoprenoid precursor rescue in P. falciparum","pmids":["28423214"],"confidence":"High","gaps":["Does not identify the direct molecular substrate whose deconjugation drives the import defect","Mechanistic link between protease activity and apicoplast biogenesis not fully resolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2017,"claim":"To connect the essential phenotype to a biochemical activity, PfOTU was implicated in membrane deconjugation of Atg8, proposing a noncanonical Atg8-processing role in apicoplast maintenance.","evidence":"Knockdown coupled with Atg8 deconjugation assays in P. falciparum","pmids":["28423214"],"confidence":"Medium","gaps":["Described as a possible function; direct causal chain from Atg8 delipidation to import defect not established","Does not quantify catalytic parameters or map the cleavage site"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"claim":"Whether PfOTU acts on canonical ubiquitin-like modifiers was tested biochemically, showing it deconjugates ubiquitin and ISG15 and is druggable at nanomolar potency.","evidence":"In vitro deconjugation assays, structural modeling, and small-molecule inhibitor screening with enzyme kinetics; western blot/flow cytometry of ubiquitinated proteins (P. falciparum, P. vivax, P. yoelii)","pmids":["34486667"],"confidence":"Medium","gaps":["Structural model is computational; no experimental structure","Cellular relevance of ubiquitin/ISG15 deconjugation versus the Atg8 role not resolved","Inhibitor selectivity against host or parasite paralogs not established"],"attribution":[{"species":"Plasmodium falciparum","strain":""},{"species":"Plasmodium vivax","strain":""},{"species":"Plasmodium yoelii","strain":""}]},{"year":2023,"claim":"The mechanistic distinction from Atg4 and the essentiality logic were resolved in the P. berghei ortholog, which cleaves Atg8 on the N-terminal side of the terminal glycine to irreversibly inactivate it and acts redundantly with Atg4.","evidence":"Individual and simultaneous gene knockouts, live localization, in vivo mouse infection, and in vitro Atg8 cleavage-site analysis in P. berghei","pmids":["37910326"],"confidence":"Medium","gaps":["Shown for the P. berghei ortholog; synthetic lethality with Atg4 not directly demonstrated for PF3D7_0923100 in P. falciparum","Individual dispensability in blood/mosquito stages contrasts with reported P. falciparum essentiality, and this species difference is unexplained","Does not define which biological process (apicoplast vs. autophagy) requires the irreversible Atg8 inactivation"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"It remains unresolved which of PfOTU's activities — Atg8 delipidation versus ubiquitin/ISG15 deconjugation — accounts for its essential apicoplast role, and how species-level differences in dispensability arise.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No experimental structure or catalytic-mutant complementation linking a specific activity to the apicoplast phenotype","Physiological ubiquitin/ISG15 substrates in the parasite not identified","Reconciliation of P. falciparum essentiality with P. berghei individual dispensability not established"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["ATG8 (SUBSTRATE)","ATG4 (REDUNDANT/SYNTHETIC-LETHAL PARTNER, SHOWN IN P. BERGHEI ORTHOLOG)","UBIQUITIN (IN VITRO SUBSTRATE)","ISG15 (IN VITRO SUBSTRATE)"],"other_free_text":["PfOTU depletion arrests P. falciparum beyond the early-schizont stage and impairs apicoplast protein import, with isoprenoid precursor supplementation used to test apicoplast specificity [#1].","Enzymatic activity is inhibited by small molecules with IC50 as low as 30 nM [#5].","In the P. berghei ortholog, individual Otu deletion is tolerated in blood and mosquito stages, but Otu+Atg4 double deletion is refractory [#3, #4]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"28423214","id":"PMC_28423214","title":"Plasmodium falciparum OTU-like cysteine protease (PfOTU) is essential for apicoplast homeostasis and associates with noncanonical role of Atg8.","date":"2017","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/28423214","citation_count":18,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["OTU","PfOTU"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"37910326","id":"PMC_37910326","title":"Regulation of Atg8 membrane deconjugation by cysteine proteases in the malaria parasite Plasmodium berghei.","date":"2023","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/37910326","citation_count":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["OTU"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34486667","id":"PMC_34486667","title":"Identification of first-in-class plasmodium OTU inhibitors with potent anti-malarial activity.","date":"2021","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/34486667","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["OTU"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4363,"output_tokens":1738,"usd":0.019579,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6771,"output_tokens":2959,"usd":0.053915,"stage2_stop_reason":"end_turn"},"total_usd":0.073494,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"PfOTU (PF3D7_0923100) localizes to vesicular compartments and associates with the apicoplast, as shown by C-terminal regulatable fluorescent affinity tagging of the native protein in P. falciparum.\",\n      \"method\": \"Regulatable fluorescent affinity tag on native protein; live imaging/subcellular localization\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with functional consequence (apicoplast association), single lab, multiple orthogonal approaches (tagging, knockdown, rescue)\",\n      \"pmids\": [\"28423214\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Knockdown of PfOTU by degradation-tag-mediated depletion causes abnormal apicoplast development, blocks parasite development beyond early-schizont stage, and impairs apicoplast protein import, establishing PfOTU as essential for apicoplast homeostasis.\",\n      \"method\": \"Degradation-tag-mediated knockdown; phenotypic analysis of apicoplast development and protein import; isoprenoid precursor rescue experiment\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with defined cellular phenotype, isoprenoid rescue confirms apicoplast-specific role, multiple orthogonal readouts in single study\",\n      \"pmids\": [\"28423214\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"PfOTU is implicated in membrane deconjugation (delipidation) of Atg8, potentially linked to apicoplast protein import, suggesting a noncanonical role for Atg8 deconjugation in apicoplast maintenance.\",\n      \"method\": \"Functional characterization via knockdown and Atg8 deconjugation assay (biochemical evidence for membrane deconjugation activity)\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — single lab, multiple methods (knockdown + Atg8 deconjugation evidence), but described as 'possible biological function' indicating partial mechanistic follow-up\",\n      \"pmids\": [\"28423214\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The Plasmodium berghei ortholog of OTU (Otu) localizes to the apicoplast; genetic disruption of Otu individually is possible, but simultaneous deletion of Otu and Atg4 is refractory, indicating synthetic lethality and overlapping essential functions in Atg8 deconjugation.\",\n      \"method\": \"Gene knockout (individual and simultaneous); live localization; in vivo and in vitro Atg8 deconjugation analysis\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis (double KO refractory), confirmed localization, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"37910326\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Otu KO parasites in P. berghei show no visible developmental defects in blood or mosquito stages, and all Otu KO sporozoites establish blood-stage infection normally, indicating Otu is dispensable individually for these lifecycle stages. In contrast, Otu cleaves the peptide bond on the N-terminal side of glycine on Atg8, thereby irreversibly inactivating Atg8 rather than recycling it, distinguishing its mechanism from Atg4.\",\n      \"method\": \"Gene knockout; in vivo mouse infection assay; in vitro Atg8 deconjugation/cleavage site analysis\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO with defined phenotypic readout and biochemical mechanistic distinction (cleavage site), single lab\",\n      \"pmids\": [\"37910326\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"P. falciparum OTU-like protein (PF3D7_0923100) demonstrates ubiquitin and ISG15 deconjugation activities in vitro, as measured by intracellular ubiquitinated protein content via western blot and flow cytometry, and its enzymatic activity can be inhibited by small molecules with IC50 values as low as 30 nM.\",\n      \"method\": \"Deconjugation assay; structural modeling; small molecule inhibitor screening; enzyme kinetics; western blot and flow cytometry for ubiquitinated proteins\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro deconjugation assay establishing enzymatic activity, but single lab and limited mechanistic follow-up; structural model is computational\",\n      \"pmids\": [\"34486667\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium vivax\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium yoelii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0923100 (PfOTU) is an OTU-domain cysteine protease that localizes to vesicular compartments and the apicoplast in P. falciparum, where it is essential for apicoplast homeostasis and protein import; it deconjugates Atg8 from membranes (and also ubiquitin/ISG15 substrates) by cleaving on the N-terminal side of the terminal glycine, thereby irreversibly inactivating Atg8 rather than recycling it, and it acts redundantly with Atg4 such that simultaneous loss of both is lethal to the parasite.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0923100 (PfOTU) is an OTU-domain cysteine deconjugating protease essential for apicoplast homeostasis in Plasmodium falciparum [#1]. The native protein localizes to vesicular compartments and associates with the apicoplast [#0], and its depletion causes abnormal apicoplast development, arrests parasites beyond the early-schizont stage, and impairs apicoplast protein import — a defect consistent with an apicoplast-specific role, as indicated by isoprenoid precursor rescue [#1]. Mechanistically, PfOTU deconjugates (delipidates) Atg8 from membranes, a noncanonical activity linked to apicoplast maintenance [#2], and in vitro it also cleaves ubiquitin and ISG15 conjugates, an activity blockable by small-molecule inhibitors with IC50 values as low as 30 nM [#5]. Work on the P. berghei ortholog shows apicoplast localization and demonstrates that Otu cleaves the peptide bond on the N-terminal side of the terminal glycine of Atg8, irreversibly inactivating Atg8 rather than recycling it, thereby distinguishing its mechanism from Atg4; individual Otu deletion is tolerated with no visible blood- or mosquito-stage defect, but simultaneous deletion of Otu and Atg4 is refractory, revealing synthetic lethality and overlapping essential functions in Atg8 deconjugation [#3, #4].\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Establishing where PfOTU acts was the first requirement for assigning it a cellular role, and native tagging placed it at vesicular compartments and the apicoplast.\",\n      \"evidence\": \"Regulatable fluorescent affinity tag on native protein with live imaging in P. falciparum\",\n      \"pmids\": [\"28423214\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab localization; does not resolve whether apicoplast association is direct or via membrane trafficking\",\n        \"Does not define the enzymatic activity operating at this site\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Whether PfOTU is functionally important was answered by depletion, which showed it is essential for apicoplast development and protein import.\",\n      \"evidence\": \"Degradation-tag knockdown with apicoplast phenotyping, protein-import readout, and isoprenoid precursor rescue in P. falciparum\",\n      \"pmids\": [\"28423214\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Does not identify the direct molecular substrate whose deconjugation drives the import defect\",\n        \"Mechanistic link between protease activity and apicoplast biogenesis not fully resolved\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"To connect the essential phenotype to a biochemical activity, PfOTU was implicated in membrane deconjugation of Atg8, proposing a noncanonical Atg8-processing role in apicoplast maintenance.\",\n      \"evidence\": \"Knockdown coupled with Atg8 deconjugation assays in P. falciparum\",\n      \"pmids\": [\"28423214\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Described as a possible function; direct causal chain from Atg8 delipidation to import defect not established\",\n        \"Does not quantify catalytic parameters or map the cleavage site\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Whether PfOTU acts on canonical ubiquitin-like modifiers was tested biochemically, showing it deconjugates ubiquitin and ISG15 and is druggable at nanomolar potency.\",\n      \"evidence\": \"In vitro deconjugation assays, structural modeling, and small-molecule inhibitor screening with enzyme kinetics; western blot/flow cytometry of ubiquitinated proteins (P. falciparum, P. vivax, P. yoelii)\",\n      \"pmids\": [\"34486667\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Structural model is computational; no experimental structure\",\n        \"Cellular relevance of ubiquitin/ISG15 deconjugation versus the Atg8 role not resolved\",\n        \"Inhibitor selectivity against host or parasite paralogs not established\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium vivax\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium yoelii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The mechanistic distinction from Atg4 and the essentiality logic were resolved in the P. berghei ortholog, which cleaves Atg8 on the N-terminal side of the terminal glycine to irreversibly inactivate it and acts redundantly with Atg4.\",\n      \"evidence\": \"Individual and simultaneous gene knockouts, live localization, in vivo mouse infection, and in vitro Atg8 cleavage-site analysis in P. berghei\",\n      \"pmids\": [\"37910326\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Shown for the P. berghei ortholog; synthetic lethality with Atg4 not directly demonstrated for PF3D7_0923100 in P. falciparum\",\n        \"Individual dispensability in blood/mosquito stages contrasts with reported P. falciparum essentiality, and this species difference is unexplained\",\n        \"Does not define which biological process (apicoplast vs. autophagy) requires the irreversible Atg8 inactivation\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved which of PfOTU's activities — Atg8 delipidation versus ubiquitin/ISG15 deconjugation — accounts for its essential apicoplast role, and how species-level differences in dispensability arise.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No experimental structure or catalytic-mutant complementation linking a specific activity to the apicoplast phenotype\",\n        \"Physiological ubiquitin/ISG15 substrates in the parasite not identified\",\n        \"Reconciliation of P. falciparum essentiality with P. berghei individual dispensability not established\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004843\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0019784\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0008234\", \"supporting_discovery_ids\": [2, 4]},\n      {\"term_id\": \"GO:0019786\", \"supporting_discovery_ids\": [2, 3, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0009507\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006914\", \"supporting_discovery_ids\": [2, 3, 4]},\n      {\"term_id\": \"GO:0016556\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"Atg8 (substrate)\",\n      \"Atg4 (redundant/synthetic-lethal partner, shown in P. berghei ortholog)\",\n      \"ubiquitin (in vitro substrate)\",\n      \"ISG15 (in vitro substrate)\"\n    ],\n    \"other_free_text\": [\n      \"PfOTU depletion arrests P. falciparum beyond the early-schizont stage and impairs apicoplast protein import, with isoprenoid precursor supplementation used to test apicoplast specificity [#1].\",\n      \"Enzymatic activity is inhibited by small molecules with IC50 as low as 30 nM [#5].\",\n      \"In the P. berghei ortholog, individual Otu deletion is tolerated in blood and mosquito stages, but Otu+Atg4 double deletion is refractory [#3, #4].\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_0923100","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 3 of 3 cited papers name other catalogue genes (PF3D7_1019900, PF3D7_1031400, PF3D7_1417300). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0923100","name":null,"product":"OTU domain-containing protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0824000","name":null,"product":"OTU domain-containing protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0721100","name":null,"product":"OTU domain-containing protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}