{"gene":"PF3D7_1311500","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2018,"finding":"P. falciparum RPT1 (PF3D7_1311500), one of six AAA+ ATPases in the 19S regulatory particle of the proteasome, directly interacts with PfPKG (cGMP-dependent protein kinase) in vitro; the interacting fragment of RPT1 carries a PfPKG consensus phosphorylation site, a peptide carrying this site competes with the RPT1 fragment for binding to PfPKG and is efficiently phosphorylated by PfPKG, indicating RPT1 is a direct substrate of PfPKG.","method":"Yeast two-hybrid library screen, in vitro binding assay, peptide competition assay, in vitro kinase assay with peptide substrates","journal":"Infection and immunity","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal in vitro binding and kinase assay with peptide competition, single lab, two orthogonal methods","pmids":["30323024"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"In a co-immunoprecipitation/mass-spectrometry (IP/MS) interactome of PbRpt3-mCherry in P. berghei trophozoite-schizont extracts, the entire putative proteasome regulatory particle ATPase Rpt subunits (Rpt1–6, including the RPT1 ortholog) were significantly co-enriched, confirming RPT1 membership in the 19S regulatory particle of the proteasome; notably, no 20S alpha or beta subunits were co-purified, suggesting the 19S–20S association is transient and dynamic in the parasite.","method":"Immunoprecipitation followed by mass spectrometry (IP/MS) in P. berghei","journal":"International journal of molecular sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/MS experiment identifying complex membership, single lab, no functional follow-up specific to RPT1","pmids":["41373862"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"P. falciparum RPT1 (PF3D7_1311500) is an AAA+ ATPase subunit of the 19S regulatory particle of the 26S proteasome that is directly phosphorylated by the cGMP-dependent protein kinase PfPKG, suggesting PKG regulation of parasite proteolysis is at least partly mediated through RPT1."},"narrative":{"mechanistic_narrative":"RPT1 (PF3D7_1311500) is one of six AAA+ ATPases of the 19S regulatory particle of the P. falciparum 26S proteasome [PMID:30323024]. Beyond its membership in the regulatory particle, RPT1 links proteasome regulation to cGMP signaling: it directly binds the cGMP-dependent protein kinase PfPKG in vitro through a fragment bearing a PfPKG consensus phosphorylation site, and a peptide spanning that site both competes for PfPKG binding and is efficiently phosphorylated by PfPKG, establishing RPT1 as a direct PfPKG substrate [PMID:30323024]. In P. berghei, an IP/MS interactome anchored on the Rpt3 ortholog co-enriched all six Rpt ATPases including the RPT1 ortholog but recovered no 20S core subunits, consistent with RPT1 being a stable component of the 19S ATPase ring whose association with the 20S core is transient [PMID:41373862]. No functional or structural characterization of RPT1's ATPase activity or its role in substrate unfolding within the parasite has been reported in the available corpus.","teleology":[{"year":2018,"claim":"Established that RPT1 physically and enzymatically connects the proteasome regulatory particle to cGMP signaling, answering whether PfPKG has a direct proteasomal substrate.","evidence":"Yeast two-hybrid screen, in vitro binding, peptide competition, and in vitro kinase assays in P. falciparum","pmids":["30323024"],"confidence":"Medium","gaps":["Phosphorylation shown on a peptide, not on full-length RPT1 in parasites","Functional consequence of RPT1 phosphorylation on proteasome activity unknown","In vivo relevance of the RPT1-PfPKG interaction not demonstrated"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Confirmed RPT1 as an integral member of the six-subunit Rpt ATPase ring of the 19S regulatory particle and indicated a dynamic 19S-20S association in the parasite.","evidence":"IP/MS interactome of PbRpt3-mCherry in P. berghei trophozoite-schizont extracts","pmids":["41373862"],"confidence":"Low","gaps":["Single Co-IP/MS experiment with no functional follow-up specific to RPT1","Shown for the P. berghei ortholog, not P. falciparum RPT1 directly","Absence of 20S subunits is interpretive; not tested by orthogonal assay"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"Whether PfPKG phosphorylation of RPT1 alters proteasome assembly, ATPase activity, or substrate degradation during the parasite life cycle remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No functional link between RPT1 phosphorylation and proteolytic output","No structural model of RPT1 within the parasite 19S particle","No genetic assessment of RPT1 essentiality or phenotype"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["19S proteasome regulatory particle (Rpt1-6 AAA+ ATPase ring)"],"partners":["PFPKG (CGMP-DEPENDENT PROTEIN KINASE)","RPT2-6 REGULATORY PARTICLE ATPASES"],"other_free_text":["RPT1 carries a PfPKG consensus phosphorylation site and is a direct PfPKG substrate in vitro (P. falciparum)","In P. berghei IP/MS, the Rpt ATPase ring co-purifies without 20S core subunits, indicating dynamic 19S-20S association"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"30323024","id":"PMC_30323024","title":"Plasmodium falciparum Cyclic GMP-Dependent Protein Kinase Interacts with a Subunit of the Parasite Proteasome.","date":"2018","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/30323024","citation_count":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPT1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41373862","id":"","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":["RPT1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38892332","id":"","title":"Post-Translational Modifications of Proteins of Malaria Parasites during the Life Cycle.","date":"2024","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38892332","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPT1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"32359426","id":"","title":"Inhibition of Resistance-Refractory P. falciparum Kinase PKG Delivers Prophylactic, Blood Stage, and Transmission-Blocking Antiplasmodial Activity.","date":"2020","source":"Cell chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/32359426","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPT1"],"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":["RPT1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"17135207","id":"","title":"CellCircuits: a database of protein network models.","date":"2006","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/17135207","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPT1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7752,"output_tokens":747,"usd":0.01723,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5374,"output_tokens":1662,"usd":0.03421,"stage2_stop_reason":"end_turn"},"total_usd":0.05144,"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\": 2018,\n      \"finding\": \"P. falciparum RPT1 (PF3D7_1311500), one of six AAA+ ATPases in the 19S regulatory particle of the proteasome, directly interacts with PfPKG (cGMP-dependent protein kinase) in vitro; the interacting fragment of RPT1 carries a PfPKG consensus phosphorylation site, a peptide carrying this site competes with the RPT1 fragment for binding to PfPKG and is efficiently phosphorylated by PfPKG, indicating RPT1 is a direct substrate of PfPKG.\",\n      \"method\": \"Yeast two-hybrid library screen, in vitro binding assay, peptide competition assay, in vitro kinase assay with peptide substrates\",\n      \"journal\": \"Infection and immunity\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal in vitro binding and kinase assay with peptide competition, single lab, two orthogonal methods\",\n      \"pmids\": [\"30323024\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In a co-immunoprecipitation/mass-spectrometry (IP/MS) interactome of PbRpt3-mCherry in P. berghei trophozoite-schizont extracts, the entire putative proteasome regulatory particle ATPase Rpt subunits (Rpt1–6, including the RPT1 ortholog) were significantly co-enriched, confirming RPT1 membership in the 19S regulatory particle of the proteasome; notably, no 20S alpha or beta subunits were co-purified, suggesting the 19S–20S association is transient and dynamic in the parasite.\",\n      \"method\": \"Immunoprecipitation followed by mass spectrometry (IP/MS) in P. berghei\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/MS experiment identifying complex membership, single lab, no functional follow-up specific to RPT1\",\n      \"pmids\": [\"41373862\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"P. falciparum RPT1 (PF3D7_1311500) is an AAA+ ATPase subunit of the 19S regulatory particle of the 26S proteasome that is directly phosphorylated by the cGMP-dependent protein kinase PfPKG, suggesting PKG regulation of parasite proteolysis is at least partly mediated through RPT1.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPT1 (PF3D7_1311500) is one of six AAA+ ATPases of the 19S regulatory particle of the P. falciparum 26S proteasome [#0]. Beyond its membership in the regulatory particle, RPT1 links proteasome regulation to cGMP signaling: it directly binds the cGMP-dependent protein kinase PfPKG in vitro through a fragment bearing a PfPKG consensus phosphorylation site, and a peptide spanning that site both competes for PfPKG binding and is efficiently phosphorylated by PfPKG, establishing RPT1 as a direct PfPKG substrate [#0]. In P. berghei, an IP/MS interactome anchored on the Rpt3 ortholog co-enriched all six Rpt ATPases including the RPT1 ortholog but recovered no 20S core subunits, consistent with RPT1 being a stable component of the 19S ATPase ring whose association with the 20S core is transient [#1]. No functional or structural characterization of RPT1's ATPase activity or its role in substrate unfolding within the parasite has been reported in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Established that RPT1 physically and enzymatically connects the proteasome regulatory particle to cGMP signaling, answering whether PfPKG has a direct proteasomal substrate.\",\n      \"evidence\": \"Yeast two-hybrid screen, in vitro binding, peptide competition, and in vitro kinase assays in P. falciparum\",\n      \"pmids\": [\n        \"30323024\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Phosphorylation shown on a peptide, not on full-length RPT1 in parasites\",\n        \"Functional consequence of RPT1 phosphorylation on proteasome activity unknown\",\n        \"In vivo relevance of the RPT1-PfPKG interaction not demonstrated\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Confirmed RPT1 as an integral member of the six-subunit Rpt ATPase ring of the 19S regulatory particle and indicated a dynamic 19S-20S association in the parasite.\",\n      \"evidence\": \"IP/MS interactome of PbRpt3-mCherry in P. berghei trophozoite-schizont extracts\",\n      \"pmids\": [\n        \"41373862\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single Co-IP/MS experiment with no functional follow-up specific to RPT1\",\n        \"Shown for the P. berghei ortholog, not P. falciparum RPT1 directly\",\n        \"Absence of 20S subunits is interpretive; not tested by orthogonal assay\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium berghei\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PfPKG phosphorylation of RPT1 alters proteasome assembly, ATPase activity, or substrate degradation during the parasite life cycle remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No functional link between RPT1 phosphorylation and proteolytic output\",\n        \"No structural model of RPT1 within the parasite 19S particle\",\n        \"No genetic assessment of RPT1 essentiality or phenotype\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0016887\",\n        \"supporting_discovery_ids\": [\n          0,\n          1\n        ]\n      },\n      {\n        \"term_id\": \"GO:0019901\",\n        \"supporting_discovery_ids\": [\n          0\n        ]\n      }\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0043161\",\n        \"supporting_discovery_ids\": [\n          0,\n          1\n        ]\n      }\n    ],\n    \"complexes\": [\n      \"19S proteasome regulatory particle (Rpt1-6 AAA+ ATPase ring)\"\n    ],\n    \"partners\": [\n      \"PfPKG (cGMP-dependent protein kinase)\",\n      \"Rpt2-6 regulatory particle ATPases\"\n    ],\n    \"other_free_text\": [\n      \"RPT1 carries a PfPKG consensus phosphorylation site and is a direct PfPKG substrate in vitro (P. falciparum)\",\n      \"In P. berghei IP/MS, the Rpt ATPase ring co-purifies without 20S core subunits, indicating dynamic 19S-20S association\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1311500","name":null,"product":"26S protease regulatory subunit 7, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1410000","name":null,"product":"26S protease regulatory subunit 7, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1411900","name":null,"product":"26S protease regulatory subunit 7, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RPT1","evaluation":null}