{"gene":"PF3D7_1215800","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2023,"finding":"Deletion of RSP9 (the single RSP9 orthologue) in Plasmodium berghei leads to failure of axoneme formation, failed male gamete release, greatly reduced fertilisation, and inefficient life cycle progression in the mosquito, demonstrating that RSP9 is necessary for axoneme assembly in Plasmodium. In contrast, the two divergent RSP9 orthologues in trypanosomatids (Trypanosoma brucei and Leishmania mexicana) are needed for flagellar beating but not for axoneme assembly, indicating contrasting selection pressures and mechanistic roles across lineages.","method":"Gene deletion (knockout) in Plasmodium berghei combined with structural analysis; comparison with trypanosomatid orthologues","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean knockout with defined cellular and developmental phenotypes (axoneme assembly failure, failed exflagellation, reduced fertilisation), replicated by orthogonal structural analysis and cross-species comparison in a peer-reviewed study","pmids":["37288670"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2024,"finding":"RSP9 was identified as a protein co-purifying with NEK1-GFP in proteomic cross-linking studies during early male gametogenesis in Plasmodium berghei, placing RSP9 in the NEK1 interaction network at the stage of basal body and axoneme formation.","method":"Proteomic cross-linking / co-immunoprecipitation pulldown of NEK1-GFP followed by mass spectrometry","journal":"PLoS biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single co-purification experiment; RSP9 is listed among many NEK1-associated proteins with no reciprocal validation or functional follow-up specific to RSP9","pmids":["39255311"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2024,"finding":"Disruption of WIG1 (a CRL4 ubiquitin ligase receptor) in Plasmodium berghei leads to downregulation of RSP9 among a set of ciliary proteins during gametocytogenesis, and RSP9 depletion is associated with impaired 9+2 axoneme symmetry but not with loss of microtubule nucleation, indicating that RSP9 protein levels are regulated by the CRL4WIG1 ubiquitin ligase pathway and that RSP9 is required for axoneme symmetry rather than initial microtubule nucleation.","method":"Proteomic analysis of WIG1-disrupted P. berghei parasites; ultrastructure expansion microscopy (U-ExM); reference to prior RSP9 deletion phenotype","journal":"mBio","confidence":"Low","confidence_rationale":"Tier 3 / Weak — RSP9 role in axoneme symmetry is cited from prior work; its downregulation upon WIG1 disruption is from a single proteomics experiment without direct RSP9-specific validation in this study","pmids":["39207167"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"In Plasmodium berghei, RSP9 (PF3D7_1215800 orthologue) is a radial spoke protein that is essential for axoneme assembly during male gametogenesis: its deletion abolishes axoneme formation, prevents male gamete exflagellation, and severely reduces fertilisation and mosquito-stage transmission, while having no effect on mitotic spindle formation; RSP9 protein levels are regulated downstream of the CRL4WIG1 ubiquitin ligase, and RSP9 co-purifies with the mitotic kinase NEK1 during early gametogenesis."},"narrative":{"mechanistic_narrative":"RSP9 (PF3D7_1215800) is a radial spoke protein required for axoneme assembly during male gametogenesis in Plasmodium; deletion of the single RSP9 orthologue in P. berghei abolishes axoneme formation, prevents male gamete release, and severely reduces fertilisation and mosquito-stage life-cycle progression [PMID:37288670]. This role is specific to flagellar axoneme construction rather than general microtubule biology, and cross-species comparison shows divergent function, as the trypanosomatid orthologues are needed for flagellar beating but not axoneme assembly [PMID:37288670]. RSP9 protein levels are regulated by the CRL4WIG1 ubiquitin ligase pathway, and RSP9 is required for 9+2 axoneme symmetry rather than for microtubule nucleation [PMID:39207167]. RSP9 also co-purifies with the mitotic kinase NEK1 during early gametogenesis, placing it in the NEK1 interaction network at the stage of basal body and axoneme formation [PMID:39255311]. Beyond these findings, no further mechanistic detail on RSP9 has been characterized in the available corpus.","teleology":[{"year":2023,"claim":"Whether Plasmodium RSP9 is required for axoneme assembly was unknown; knockout established it as necessary for flagellar axoneme formation and male gamete transmission, and revealed lineage-divergent roles relative to trypanosomatids.","evidence":"Gene deletion in P. berghei with structural analysis and cross-species orthologue comparison","pmids":["37288670"],"confidence":"High","gaps":["Does not define the specific radial-spoke substructure or partner proteins RSP9 contacts within the axoneme","No molecular mechanism for how RSP9 loss blocks axoneme assembly","Phenotype established in P. berghei, not directly in P. falciparum PF3D7_1215800"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2024,"claim":"Whether RSP9 associates with the gametogenesis kinase machinery was unknown; a NEK1-GFP pulldown placed RSP9 in the NEK1 interaction network during early male gametogenesis.","evidence":"Proteomic cross-linking / co-IP of NEK1-GFP with mass spectrometry in P. berghei","pmids":["39255311"],"confidence":"Low","gaps":["Single co-purification without reciprocal validation or RSP9-specific functional follow-up","Direct versus indirect nature of the NEK1 association is undetermined","Functional consequence of the NEK1-RSP9 association is not tested"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2024,"claim":"How RSP9 abundance is controlled and which structural feature it supports was unclear; WIG1 disruption showed RSP9 is downregulated among ciliary proteins and required for axoneme symmetry rather than microtubule nucleation.","evidence":"Proteomics of WIG1-disrupted P. berghei plus U-ExM ultrastructure, with the symmetry phenotype cited from prior RSP9 deletion work","pmids":["39207167"],"confidence":"Low","gaps":["RSP9 downregulation from a single proteomics dataset without direct RSP9-specific validation in this study","Whether RSP9 is a direct CRL4WIG1 ubiquitination target is not shown","Mechanism linking RSP9 level to 9+2 symmetry is not resolved"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"The direct radial-spoke binding partners, structural placement, and the molecular basis by which RSP9 enforces 9+2 axoneme symmetry in Plasmodium remain undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No reconstituted or structural model of RSP9 within the radial spoke","No validated direct interaction partners for RSP9","Function not directly demonstrated for the P. falciparum PF3D7_1215800 gene itself"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Radial spoke","NEK1 interaction network (co-purification)"],"partners":["NEK1 (CO-PURIFICATION)","CRL4WIG1 UBIQUITIN LIGASE PATHWAY (REGULATES RSP9 LEVELS)"],"other_free_text":["RSP9 (PF3D7_1215800) is characterized primarily through its P. berghei orthologue; findings are attributed to P. berghei, not directly to the P. falciparum gene.","RSP9 is required for 9+2 axoneme symmetry but dispensable for microtubule nucleation and mitotic spindle formation.","Trypanosomatid RSP9 orthologues function in flagellar beating rather than axoneme assembly, indicating lineage-divergent roles."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"37288670","id":"PMC_37288670","title":"Radial spoke protein 9 is necessary for axoneme assembly in Plasmodium but not in trypanosomatid parasites.","date":"2023","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/37288670","citation_count":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RSP9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41218080","id":"","title":"Plasmodium actin-like proteins are essential for DNA segregation during male gametogenesis and malaria transmission.","date":"2025","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/41218080","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RSP9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38563493","id":"","title":"The molecular mechanisms driving Plasmodium cell division.","date":"2024","source":"Biochemical Society transactions","url":"https://pubmed.ncbi.nlm.nih.gov/38563493","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RSP9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39207167","id":"","title":"A multistage Plasmodium CRL4WIG1 ubiquitin ligase is critical for the formation of functional microtubule organization centers in microgametocytes.","date":"2024","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/39207167","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RSP9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39255311","id":"","title":"Plasmodium NEK1 coordinates MTOC organisation and kinetochore attachment during rapid mitosis in male gamete formation.","date":"2024","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/39255311","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RSP9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25974046","id":"","title":"The more we know, the more we have to discover: an exciting future for understanding cilia and ciliopathies.","date":"2015","source":"Cilia","url":"https://pubmed.ncbi.nlm.nih.gov/25974046","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RSP9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7843,"output_tokens":1096,"usd":0.019984,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5905,"output_tokens":2042,"usd":0.040287,"stage2_stop_reason":"end_turn"},"total_usd":0.060271,"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\": 2023,\n      \"finding\": \"Deletion of RSP9 (the single RSP9 orthologue) in Plasmodium berghei leads to failure of axoneme formation, failed male gamete release, greatly reduced fertilisation, and inefficient life cycle progression in the mosquito, demonstrating that RSP9 is necessary for axoneme assembly in Plasmodium. In contrast, the two divergent RSP9 orthologues in trypanosomatids (Trypanosoma brucei and Leishmania mexicana) are needed for flagellar beating but not for axoneme assembly, indicating contrasting selection pressures and mechanistic roles across lineages.\",\n      \"method\": \"Gene deletion (knockout) in Plasmodium berghei combined with structural analysis; comparison with trypanosomatid orthologues\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean knockout with defined cellular and developmental phenotypes (axoneme assembly failure, failed exflagellation, reduced fertilisation), replicated by orthogonal structural analysis and cross-species comparison in a peer-reviewed study\",\n      \"pmids\": [\"37288670\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RSP9 was identified as a protein co-purifying with NEK1-GFP in proteomic cross-linking studies during early male gametogenesis in Plasmodium berghei, placing RSP9 in the NEK1 interaction network at the stage of basal body and axoneme formation.\",\n      \"method\": \"Proteomic cross-linking / co-immunoprecipitation pulldown of NEK1-GFP followed by mass spectrometry\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single co-purification experiment; RSP9 is listed among many NEK1-associated proteins with no reciprocal validation or functional follow-up specific to RSP9\",\n      \"pmids\": [\"39255311\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Disruption of WIG1 (a CRL4 ubiquitin ligase receptor) in Plasmodium berghei leads to downregulation of RSP9 among a set of ciliary proteins during gametocytogenesis, and RSP9 depletion is associated with impaired 9+2 axoneme symmetry but not with loss of microtubule nucleation, indicating that RSP9 protein levels are regulated by the CRL4WIG1 ubiquitin ligase pathway and that RSP9 is required for axoneme symmetry rather than initial microtubule nucleation.\",\n      \"method\": \"Proteomic analysis of WIG1-disrupted P. berghei parasites; ultrastructure expansion microscopy (U-ExM); reference to prior RSP9 deletion phenotype\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — RSP9 role in axoneme symmetry is cited from prior work; its downregulation upon WIG1 disruption is from a single proteomics experiment without direct RSP9-specific validation in this study\",\n      \"pmids\": [\"39207167\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"In Plasmodium berghei, RSP9 (PF3D7_1215800 orthologue) is a radial spoke protein that is essential for axoneme assembly during male gametogenesis: its deletion abolishes axoneme formation, prevents male gamete exflagellation, and severely reduces fertilisation and mosquito-stage transmission, while having no effect on mitotic spindle formation; RSP9 protein levels are regulated downstream of the CRL4WIG1 ubiquitin ligase, and RSP9 co-purifies with the mitotic kinase NEK1 during early gametogenesis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RSP9 (PF3D7_1215800) is a radial spoke protein required for axoneme assembly during male gametogenesis in Plasmodium; deletion of the single RSP9 orthologue in P. berghei abolishes axoneme formation, prevents male gamete release, and severely reduces fertilisation and mosquito-stage life-cycle progression [#0]. This role is specific to flagellar axoneme construction rather than general microtubule biology, and cross-species comparison shows divergent function, as the trypanosomatid orthologues are needed for flagellar beating but not axoneme assembly [#0]. RSP9 protein levels are regulated by the CRL4WIG1 ubiquitin ligase pathway, and RSP9 is required for 9+2 axoneme symmetry rather than for microtubule nucleation [#2]. RSP9 also co-purifies with the mitotic kinase NEK1 during early gametogenesis, placing it in the NEK1 interaction network at the stage of basal body and axoneme formation [#1]. Beyond these findings, no further mechanistic detail on RSP9 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether Plasmodium RSP9 is required for axoneme assembly was unknown; knockout established it as necessary for flagellar axoneme formation and male gamete transmission, and revealed lineage-divergent roles relative to trypanosomatids.\",\n      \"evidence\": \"Gene deletion in P. berghei with structural analysis and cross-species orthologue comparison\",\n      \"pmids\": [\"37288670\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Does not define the specific radial-spoke substructure or partner proteins RSP9 contacts within the axoneme\",\n        \"No molecular mechanism for how RSP9 loss blocks axoneme assembly\",\n        \"Phenotype established in P. berghei, not directly in P. falciparum PF3D7_1215800\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Whether RSP9 associates with the gametogenesis kinase machinery was unknown; a NEK1-GFP pulldown placed RSP9 in the NEK1 interaction network during early male gametogenesis.\",\n      \"evidence\": \"Proteomic cross-linking / co-IP of NEK1-GFP with mass spectrometry in P. berghei\",\n      \"pmids\": [\"39255311\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single co-purification without reciprocal validation or RSP9-specific functional follow-up\",\n        \"Direct versus indirect nature of the NEK1 association is undetermined\",\n        \"Functional consequence of the NEK1-RSP9 association is not tested\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"How RSP9 abundance is controlled and which structural feature it supports was unclear; WIG1 disruption showed RSP9 is downregulated among ciliary proteins and required for axoneme symmetry rather than microtubule nucleation.\",\n      \"evidence\": \"Proteomics of WIG1-disrupted P. berghei plus U-ExM ultrastructure, with the symmetry phenotype cited from prior RSP9 deletion work\",\n      \"pmids\": [\"39207167\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"RSP9 downregulation from a single proteomics dataset without direct RSP9-specific validation in this study\",\n        \"Whether RSP9 is a direct CRL4WIG1 ubiquitination target is not shown\",\n        \"Mechanism linking RSP9 level to 9+2 symmetry is not resolved\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct radial-spoke binding partners, structural placement, and the molecular basis by which RSP9 enforces 9+2 axoneme symmetry in Plasmodium remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No reconstituted or structural model of RSP9 within the radial spoke\",\n        \"No validated direct interaction partners for RSP9\",\n        \"Function not directly demonstrated for the P. falciparum PF3D7_1215800 gene itself\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0001534\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0007288\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0035082\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"complexes\": [\"Radial spoke\", \"NEK1 interaction network (co-purification)\"],\n    \"partners\": [\"NEK1 (co-purification)\", \"CRL4WIG1 ubiquitin ligase pathway (regulates RSP9 levels)\"],\n    \"other_free_text\": [\n      \"RSP9 (PF3D7_1215800) is characterized primarily through its P. berghei orthologue; findings are attributed to P. berghei, not directly to the P. falciparum gene.\",\n      \"RSP9 is required for 9+2 axoneme symmetry but dispensable for microtubule nucleation and mitotic spindle formation.\",\n      \"Trypanosomatid RSP9 orthologues function in flagellar beating rather than axoneme assembly, indicating lineage-divergent roles.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1215800","name":null,"product":"radial spoke protein 9, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1431500","name":null,"product":"radial spoke head protein 9, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1435300","name":null,"product":"radial spoke head protein 9, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RSP9","evaluation":null}