{"gene":"PF3D7_0413600","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2025,"finding":"P. berghei RPT3 (ortholog of PF3D7_0413600) directly binds the Protein Phosphatase 1 catalytic subunit (PP1c) via its RVxF motifs, and enhances PP1c activity both in vitro and in a Xenopus oocyte heterologous model. The interaction and regulatory function were shown to occur outside of the proteasome context, and ATP-binding capacity of RPT3 also contributes to its phosphatase regulatory activity.","method":"Co-immunoprecipitation/binding assay, in vitro phosphatase activity assay, Xenopus oocyte heterologous expression model, RVxF motif mutagenesis","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 1-2 / Weak — in vitro phosphatase assay plus heterologous model with mutagenesis, but single lab, single paper, and performed in P. berghei ortholog rather than P. falciparum RPT3 directly","pmids":["41373862"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"finding":"Reverse genetic studies in P. berghei suggest an essential role for RPT3 during the erythrocytic cycle. Interactome analysis confirmed that RPT3 belongs to the 19S regulatory particle of the proteasome and may interact with proteins involved in phospholipid binding.","method":"Reverse genetics (attempted gene knockout/knockdown), interactome/mass spectrometry analysis","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2-3 / Weak — reverse genetics with defined phenotypic readout and interactome MS, single lab, single paper, performed in P. berghei ortholog","pmids":["41373862"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"The P. berghei ortholog of RPT3 (PF3D7_0413600) is a component of the 19S regulatory particle of the 26S proteasome that also functions outside the proteasome by directly binding Protein Phosphatase 1 catalytic subunit (PP1c) via RVxF motifs, enhancing PP1c activity in an ATP-binding-dependent manner, and is essential for parasite survival during the erythrocytic cycle."},"narrative":{"mechanistic_narrative":"RPT3 (PF3D7_0413600) is a component of the 19S regulatory particle of the 26S proteasome that also carries out a moonlighting regulatory function in phosphatase signaling, as established through work on its P. berghei ortholog [PMID:41373862]. In P. berghei, RPT3 directly binds the Protein Phosphatase 1 catalytic subunit (PP1c) via RVxF motifs and enhances PP1c activity both in vitro and in a Xenopus oocyte heterologous system, with this interaction and regulatory effect occurring outside the proteasome context; RPT3's ATP-binding capacity contributes to this phosphatase regulatory activity [PMID:41373862]. Reverse genetic studies in P. berghei indicate that RPT3 is essential during the erythrocytic cycle, and interactome analysis confirms both its membership in the 19S regulatory particle and potential association with phospholipid-binding proteins [PMID:41373862]. Beyond these findings in the P. berghei ortholog, no further mechanistic detail specific to PF3D7_0413600 has been characterized in the available corpus.","teleology":[{"year":2025,"claim":"Whether RPT3 functions only as a proteasome subunit or also acts independently was unknown; showing direct PP1c binding via RVxF motifs and enhancement of phosphatase activity outside the proteasome established a moonlighting regulatory role.","evidence":"Co-immunoprecipitation/binding assay, in vitro phosphatase activity assay, Xenopus oocyte heterologous expression, and RVxF motif mutagenesis on the P. berghei ortholog","pmids":["41373862"],"confidence":"Medium","gaps":["Demonstrated in the P. berghei ortholog rather than P. falciparum PF3D7_0413600 directly","Single lab, single paper without independent replication","The physiological substrates and downstream signaling consequences of RPT3-enhanced PP1c activity are not defined"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"claim":"Whether RPT3 is required for parasite growth and how it associates within the proteasome was unresolved; reverse genetics and interactome analysis established its essentiality during the erythrocytic cycle and confirmed its place in the 19S regulatory particle.","evidence":"Attempted gene knockout/knockdown reverse genetics with phenotypic readout plus interactome mass spectrometry in the P. berghei ortholog","pmids":["41373862"],"confidence":"Medium","gaps":["Shown in the P. berghei ortholog, not directly in P. falciparum PF3D7_0413600","The functional significance of the potential interaction with phospholipid-binding proteins is not characterized","Essentiality was inferred from failed disruption rather than conditional depletion with a defined stage-specific arrest"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"It remains unknown whether the PP1c-regulatory moonlighting function and 19S proteasome roles of RPT3 are conserved in P. falciparum PF3D7_0413600 itself and what its endogenous phosphatase substrates and physiological outputs are.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No direct experimental characterization of P. falciparum PF3D7_0413600","No identified downstream substrates of the RPT3-PP1c regulatory axis","No structural model of the RPT3-PP1c interaction"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["19S proteasome regulatory particle"],"partners":["PROTEIN PHOSPHATASE 1 CATALYTIC SUBUNIT (PP1C)"],"other_free_text":["Binds PP1c through RVxF docking motifs and enhances PP1c activity outside the proteasome context (shown in the P. berghei ortholog)","ATP-binding capacity contributes to RPT3 phosphatase-regulatory activity (P. berghei ortholog)","Essential during the erythrocytic cycle by reverse genetics (P. berghei ortholog)","Interactome links RPT3 to proteins involved in phospholipid binding (P. berghei ortholog)","All current mechanistic evidence derives from the P. berghei ortholog; direct characterization of P. falciparum PF3D7_0413600 is absent from the corpus"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"41373862","id":"PMC_41373862","title":"Characterization of the Regulatory AAA-ATPase Subunit Rpt3 in Plasmodium berghei as an Activator of Protein Phosphatase 1.","date":"2025","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41373862","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPT3","PbRPT3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38404287","id":"","title":"Mutation in the 26S proteasome regulatory subunit rpn2 gene in Plasmodium falciparum confers resistance to artemisinin.","date":"2024","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/38404287","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPT3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41301442","id":"","title":"Cleaving Expectations: A Review of Proteasome Functional and Catalytic Diversity.","date":"2025","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/41301442","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPT3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23282319","id":"","title":"Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum.","date":"2012","source":"BMC systems biology","url":"https://pubmed.ncbi.nlm.nih.gov/23282319","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPT3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19374766","id":"","title":"A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation.","date":"2009","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/19374766","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPT3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7301,"output_tokens":691,"usd":0.016134,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5328,"output_tokens":1852,"usd":0.03647,"stage2_stop_reason":"end_turn"},"total_usd":0.052604,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2025,\n      \"finding\": \"P. berghei RPT3 (ortholog of PF3D7_0413600) directly binds the Protein Phosphatase 1 catalytic subunit (PP1c) via its RVxF motifs, and enhances PP1c activity both in vitro and in a Xenopus oocyte heterologous model. The interaction and regulatory function were shown to occur outside of the proteasome context, and ATP-binding capacity of RPT3 also contributes to its phosphatase regulatory activity.\",\n      \"method\": \"Co-immunoprecipitation/binding assay, in vitro phosphatase activity assay, Xenopus oocyte heterologous expression model, RVxF motif mutagenesis\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Weak — in vitro phosphatase assay plus heterologous model with mutagenesis, but single lab, single paper, and performed in P. berghei ortholog rather than P. falciparum RPT3 directly\",\n      \"pmids\": [\"41373862\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Reverse genetic studies in P. berghei suggest an essential role for RPT3 during the erythrocytic cycle. Interactome analysis confirmed that RPT3 belongs to the 19S regulatory particle of the proteasome and may interact with proteins involved in phospholipid binding.\",\n      \"method\": \"Reverse genetics (attempted gene knockout/knockdown), interactome/mass spectrometry analysis\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Weak — reverse genetics with defined phenotypic readout and interactome MS, single lab, single paper, performed in P. berghei ortholog\",\n      \"pmids\": [\"41373862\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"The P. berghei ortholog of RPT3 (PF3D7_0413600) is a component of the 19S regulatory particle of the 26S proteasome that also functions outside the proteasome by directly binding Protein Phosphatase 1 catalytic subunit (PP1c) via RVxF motifs, enhancing PP1c activity in an ATP-binding-dependent manner, and is essential for parasite survival during the erythrocytic cycle.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPT3 (PF3D7_0413600) is a component of the 19S regulatory particle of the 26S proteasome that also carries out a moonlighting regulatory function in phosphatase signaling, as established through work on its P. berghei ortholog [#0, #1]. In P. berghei, RPT3 directly binds the Protein Phosphatase 1 catalytic subunit (PP1c) via RVxF motifs and enhances PP1c activity both in vitro and in a Xenopus oocyte heterologous system, with this interaction and regulatory effect occurring outside the proteasome context; RPT3's ATP-binding capacity contributes to this phosphatase regulatory activity [#0]. Reverse genetic studies in P. berghei indicate that RPT3 is essential during the erythrocytic cycle, and interactome analysis confirms both its membership in the 19S regulatory particle and potential association with phospholipid-binding proteins [#1]. Beyond these findings in the P. berghei ortholog, no further mechanistic detail specific to PF3D7_0413600 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether RPT3 functions only as a proteasome subunit or also acts independently was unknown; showing direct PP1c binding via RVxF motifs and enhancement of phosphatase activity outside the proteasome established a moonlighting regulatory role.\",\n      \"evidence\": \"Co-immunoprecipitation/binding assay, in vitro phosphatase activity assay, Xenopus oocyte heterologous expression, and RVxF motif mutagenesis on the P. berghei ortholog\",\n      \"pmids\": [\"41373862\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Demonstrated in the P. berghei ortholog rather than P. falciparum PF3D7_0413600 directly\",\n        \"Single lab, single paper without independent replication\",\n        \"The physiological substrates and downstream signaling consequences of RPT3-enhanced PP1c activity are not defined\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium berghei\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether RPT3 is required for parasite growth and how it associates within the proteasome was unresolved; reverse genetics and interactome analysis established its essentiality during the erythrocytic cycle and confirmed its place in the 19S regulatory particle.\",\n      \"evidence\": \"Attempted gene knockout/knockdown reverse genetics with phenotypic readout plus interactome mass spectrometry in the P. berghei ortholog\",\n      \"pmids\": [\"41373862\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Shown in the P. berghei ortholog, not directly in P. falciparum PF3D7_0413600\",\n        \"The functional significance of the potential interaction with phospholipid-binding proteins is not characterized\",\n        \"Essentiality was inferred from failed disruption rather than conditional depletion with a defined stage-specific arrest\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium berghei\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether the PP1c-regulatory moonlighting function and 19S proteasome roles of RPT3 are conserved in P. falciparum PF3D7_0413600 itself and what its endogenous phosphatase substrates and physiological outputs are.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct experimental characterization of P. falciparum PF3D7_0413600\",\n        \"No identified downstream substrates of the RPT3-PP1c regulatory axis\",\n        \"No structural model of the RPT3-PP1c interaction\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004865\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005524\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0019903\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0043161\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [\n      \"19S proteasome regulatory particle\"\n    ],\n    \"partners\": [\n      \"Protein Phosphatase 1 catalytic subunit (PP1c)\"\n    ],\n    \"other_free_text\": [\n      \"Binds PP1c through RVxF docking motifs and enhances PP1c activity outside the proteasome context (shown in the P. berghei ortholog)\",\n      \"ATP-binding capacity contributes to RPT3 phosphatase-regulatory activity (P. berghei ortholog)\",\n      \"Essential during the erythrocytic cycle by reverse genetics (P. berghei ortholog)\",\n      \"Interactome links RPT3 to proteins involved in phospholipid binding (P. berghei ortholog)\",\n      \"All current mechanistic evidence derives from the P. berghei ortholog; direct characterization of P. falciparum PF3D7_0413600 is absent from the corpus\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0413600","name":null,"product":"26S protease regulatory subunit 6B, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0715600","name":null,"product":"26S protease regulatory subunit 6B, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0505200","name":null,"product":"26S protease regulatory subunit 6B, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RPT3","evaluation":null}