{"gene":"PF3D7_0517300","run_date":"2026-09-07T10:55:52","timeline":{"discoveries":[{"year":2010,"finding":"PfSR1 (PF3D7_0517300) was identified as a substrate of PfSRPK1 (a novel P. falciparum splicing-related kinase); PfSR1 interacts with RNA, and PfSRPK1 modulates PfSR1's RNA binding activity. Both PfSRPK1 and PfSR1 localize to the nucleus early in parasite development.","method":"In vitro kinase assay (substrate identification), RNA-binding assay, nuclear fractionation/localization","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct substrate identification by kinase assay and RNA-binding modulation shown, single lab with two orthogonal methods","pmids":["20870716"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"finding":"PfSR1 can mediate RNA splicing in vitro and functions as an alternative splicing factor in mini-gene in vivo systems, similar to mammalian SRSF1. The predicted RS domain of PfSR1 is essential for its localization to the nucleus. Over-expression of pfsr1 influences alternative splicing of P. falciparum genes in vivo, and proper regulation of pfsr1 is required for parasite proliferation in human RBCs.","method":"In vitro splicing assay, mini-gene reporter system, PfSR1-myc tagging with live-cell imaging, RS-domain deletion mutagenesis, inducible overexpression with AS analysis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (in vitro splicing, in vivo mini-gene, mutagenesis of RS domain, inducible overexpression) in a single rigorous study","pmids":["22885299"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"PfSR1 localizes adjacent to Nuclear Pore Complex (NPC) clusters in the nucleus of early-stage parasites. RNA immunoprecipitation followed by microarray (RIP-chip) identified endogenous RNA targets of PfSR1; bioinformatic analysis revealed common sequence motifs, and RNA-EMSAs confirmed PfSR1 preferentially binds RNA molecules containing these motifs. PfSR1 regulates not only alternative splicing but also steady-state mRNA levels of transcripts containing these motifs in vivo.","method":"Live-cell imaging/fluorescence microscopy, RIP-chip (RNA immunoprecipitation + microarray), RNA-EMSA, inducible overexpression system","journal":"Molecular microbiology","confidence":"High","confidence_rationale":"Tier 2 / Strong — RIP-chip for endogenous target identification combined with RNA-EMSA validation and in vivo mRNA level changes, multiple orthogonal methods in single study","pmids":["25807998"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"finding":"PfSR1 plays an unexpected role in DNA repair in P. falciparum: using an inducible and reversible expression system, PfSR1 was shown to be recruited to foci of DNA damage. Loss of PfSR1 does not impair basal parasite viability but is essential for recovery from DNA-damaging agents and from artemisinin exposure, establishing PfSR1 as required for the DNA damage response.","method":"Inducible/reversible knockdown system, immunofluorescence assay for DNA damage foci recruitment, DNA-damaging agent and artemisinin challenge assays","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — inducible reversible system with multiple functional readouts (foci recruitment, chemical challenge with DNA-damaging agents and artemisinin), multiple orthogonal methods in single study","pmids":["34291805"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"finding":"SR1 (P. berghei ortholog of PF3D7_0517300) is essential for asexual development of malaria parasites. NAB2 and SR1 (but not THO4, NPL3, or GBP2) play essential roles in asexual development of P. berghei.","method":"Genetic knockout/knockdown with developmental phenotype assessment in P. berghei","journal":"Frontiers in cellular and infection microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean genetic loss-of-function with defined developmental phenotype, single lab","pmids":["34604117"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2018,"finding":"The N-terminal RRM1 of PfSR1 recognizes RNA with semi-specificity for pyrimidines: a conserved tyrosine on β1 and a glutamate on β4 mediate specific recognition of a cytosine 5' of one or more pyrimidines, while affinity is conferred by insertion of a 3' pyrimidine into a positively charged pocket. RRM1 binds RNA with moderate affinity and retains fast dynamics. The purine preference of PfSR1 was ascertained to reside in the C-terminal pseudo-RRM (RRM2), which binds RNA non-canonically and with greater affinity than RRM1. The two RRMs thus show complementary RNA sequence recognition.","method":"NMR solution structure of RRM1–RNA complex, isothermal titration calorimetry (ITC), NMR chemical shift perturbation mapping, site-specific mutagenesis inference from structural data","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR structure of protein–RNA complex combined with ITC binding measurements and CSP mapping, single lab but multiple orthogonal structural/biophysical methods","pmids":["30500338"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2026,"finding":"PbSR1 (P. berghei ortholog of PF3D7_0517300) localizes predominantly to the nucleus but also to the cytoplasm. IP-MS identified PbSR1 interacting partners including nuclear RNA-binding proteins and small nuclear ribonucleoproteins, as well as cytoplasmic rhoptry proteins RhopH1 (Clag3), RhopH2, and RhopH3. Live-cell imaging showed co-localization of PbSR1 and RhopH2 in the cytoplasm of trophozoites and gametocytes but not in mature schizonts or merozoites.","method":"Immunoprecipitation coupled to mass spectrometry (IP-MS) of GFP-tagged PbSR1, live-cell fluorescence imaging of co-expressed PbSR1::GFP and RhopH2::mCherry, western blot","journal":"Malaria journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal IP-MS with live-cell imaging validation, single lab, two orthogonal methods","pmids":["41634752"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":"ANKA"}]}],"current_model":"PfSR1/PbSR1 (PF3D7_0517300) is a bona fide SR-family splicing factor that binds RNA through complementary mechanisms of its two RRM domains (RRM1 preferring pyrimidines, RRM2 preferring purines), mediates alternative splicing and regulates steady-state mRNA levels by recognizing specific sequence motifs near Nuclear Pore Complexes, requires its RS domain for nuclear localization, is phosphorylated by PfSRPK1 (which modulates its RNA binding), is essential for asexual parasite proliferation, and additionally plays an unexpected role in DNA repair by being recruited to DNA damage foci and enabling parasite recovery from DNA-damaging agents and artemisinin; in P. berghei it also interacts with rhoptry complex proteins RhopH1/2/3 in the cytoplasm of trophozoites and gametocytes."},"narrative":{"mechanistic_narrative":"PF3D7_0517300 (PfSR1/PbSR1) is a serine/arginine-rich splicing factor that governs RNA processing in malaria parasites, functioning analogously to mammalian SRSF1 by mediating constitutive and alternative splicing and additionally regulating steady-state mRNA levels [PMID:22885299, PMID:25807998]. It engages RNA through two RRM domains with complementary sequence preferences: the N-terminal RRM1 recognizes pyrimidines through a conserved tyrosine and glutamate that specify a cytosine 5' of pyrimidines with a 3' pyrimidine inserted into a positively charged pocket, while the C-terminal pseudo-RRM (RRM2) binds purines non-canonically and with higher affinity [PMID:30500338]. Endogenously, PfSR1 binds transcripts bearing specific sequence motifs and controls both their splicing and abundance in vivo, acting from a nuclear position adjacent to Nuclear Pore Complex clusters [PMID:25807998]. Its RS domain is required for nuclear localization [PMID:22885299], and its RNA-binding activity is modulated by phosphorylation by the splicing-related kinase PfSRPK1 [PMID:20870716]. Proper regulation of the factor is required for asexual proliferation in erythrocytes, and its P. berghei ortholog is essential for asexual development [PMID:22885299, PMID:34604117]. Beyond splicing, PfSR1 has an unexpected role in the DNA damage response: it is recruited to DNA damage foci and, while dispensable for basal viability, is required for parasite recovery from DNA-damaging agents and from artemisinin [PMID:34291805]. In P. berghei, PbSR1 localizes to both nucleus and cytoplasm and, in addition to nuclear RNA-binding partners and small nuclear ribonucleoproteins, co-localizes with the rhoptry proteins RhopH1/2/3 in the cytoplasm of trophozoites and gametocytes [PMID:41634752].","teleology":[{"year":2010,"claim":"Establishing that PF3D7_0517300 is an RNA-binding protein and a kinase substrate placed it in a splicing-regulatory context and identified an upstream regulator of its activity.","evidence":"In vitro kinase assay, RNA-binding assay, and nuclear fractionation in P. falciparum","pmids":["20870716"],"confidence":"Medium","gaps":["Phosphosites on PfSR1 not mapped","Functional consequence of PfSRPK1 phosphorylation on splicing not tested in vivo"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"claim":"Demonstrating splicing activity, RS-domain-dependent nuclear localization, and a proliferation requirement defined PF3D7_0517300 as a bona fide SR splicing factor essential for the parasite.","evidence":"In vitro splicing, mini-gene reporters, RS-domain deletion, and inducible overexpression in P. falciparum","pmids":["22885299"],"confidence":"High","gaps":["Direct endogenous splicing targets not yet identified","Mechanism linking splicing defects to proliferation loss unresolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Identifying endogenous RNA targets and a bound sequence motif showed PF3D7_0517300 regulates both alternative splicing and steady-state mRNA levels from a position at the nuclear periphery.","evidence":"RIP-chip, RNA-EMSA, and live-cell imaging near NPC clusters in P. falciparum","pmids":["25807998"],"confidence":"High","gaps":["Functional consequence of NPC-adjacent localization not mechanistically dissected","How motif recognition selects splicing vs. mRNA-stability outcomes unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"claim":"Structural and biophysical dissection of the two RRMs explained how PF3D7_0517300 achieves broad RNA recognition through complementary pyrimidine- and purine-preferring modules.","evidence":"NMR structure of RRM1–RNA complex, ITC, and chemical shift perturbation mapping in P. falciparum","pmids":["30500338"],"confidence":"High","gaps":["Full-length tandem-RRM RNA complex not resolved","Structural basis of RRM2 non-canonical binding not directly determined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"claim":"An inducible/reversible system revealed a moonlighting role in the DNA damage response, showing PF3D7_0517300 is recruited to damage foci and required for recovery from genotoxic and artemisinin stress despite being dispensable for basal viability.","evidence":"Inducible/reversible knockdown, immunofluorescence of damage foci, and DNA-damaging-agent/artemisinin challenge in P. falciparum","pmids":["34291805"],"confidence":"High","gaps":["Molecular mechanism linking an SR splicing factor to DNA repair unresolved","Whether the repair role depends on RNA binding or splicing activity not determined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"claim":"Genetic loss-of-function in P. berghei confirmed the ortholog's essentiality for asexual development, distinguishing it from other mRNA-export/RNA-binding factors that were dispensable.","evidence":"Genetic knockout/knockdown with developmental phenotyping in P. berghei","pmids":["34604117"],"confidence":"Medium","gaps":["Stage of developmental arrest not molecularly characterized","Whether essentiality reflects splicing function specifically not addressed"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2026,"claim":"Interactome and imaging in P. berghei extended the factor's associations beyond nuclear RNA machinery to an unexpected cytoplasmic co-localization with rhoptry proteins in specific developmental stages.","evidence":"IP-MS of GFP-tagged PbSR1 and live-cell co-imaging with RhopH2 in P. berghei ANKA","pmids":["41634752"],"confidence":"Medium","gaps":["Functional significance of the RhopH interaction unknown","Whether cytoplasmic association is direct or indirect not established","Stage-specificity mechanism unexplained"],"attribution":[{"species":"Plasmodium berghei","strain":"ANKA"}]},{"year":null,"claim":"How PF3D7_0517300 mechanistically bridges its established splicing/mRNA-regulatory function to its DNA damage response role and its cytoplasmic rhoptry-protein association remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No mechanism connecting splicing activity to DNA repair recruitment","Functional role of RhopH co-localization untested","Cross-species reconciliation of nuclear vs. cytoplasmic roles absent"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["PFSRPK1 (KINASE, PHOSPHORYLATES PFSR1; P. FALCIPARUM)","RHOPH1/CLAG3 (P. BERGHEI, CYTOPLASMIC CO-LOCALIZATION)","RHOPH2 (P. BERGHEI, CYTOPLASMIC CO-LOCALIZATION)","RHOPH3 (P. BERGHEI)","NUCLEAR RNA-BINDING PROTEINS AND SMALL NUCLEAR RIBONUCLEOPROTEINS (P. BERGHEI IP-MS)"],"other_free_text":["Two-RRM architecture with complementary RNA sequence preference: RRM1 pyrimidine-preferring, RRM2 (pseudo-RRM) purine-preferring [#5]","RS domain required for nuclear localization [#1]","Regulates both alternative splicing and steady-state mRNA levels of motif-containing transcripts [#2]","Essential for asexual proliferation in P. falciparum and asexual development in P. berghei [#1, #4]","Required for recovery from DNA-damaging agents and artemisinin; recruited to DNA damage foci [#3]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"20870716","id":"PMC_20870716","title":"PfSRPK1, a novel splicing-related kinase from Plasmodium falciparum.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20870716","citation_count":31,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22885299","id":"PMC_22885299","title":"A novel Plasmodium falciparum SR protein is an alternative splicing factor required for the parasites' proliferation in human erythrocytes.","date":"2012","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/22885299","citation_count":29,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25807998","id":"PMC_25807998","title":"PfSR1 controls alternative splicing and steady-state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs.","date":"2015","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/25807998","citation_count":18,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34291805","id":"PMC_34291805","title":"An SR protein is essential for activating DNA repair in malaria parasites.","date":"2021","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/34291805","citation_count":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34604117","id":"PMC_34604117","title":"Roles and Cellular Localization of GBP2 and NAB2 During the Blood Stage of Malaria Parasites.","date":"2021","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/34604117","citation_count":6,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["serine/arginine-rich splicing factor 1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"30500338","id":"PMC_30500338","title":"The N-terminal RNA Recognition Motif of PfSR1 Confers Semi-specificity for Pyrimidines during RNA Recognition.","date":"2018","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/30500338","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41634752","id":"PMC_41634752","title":"Identification of serine/arginine-rich splicing factor 1-interacting proteins in Plasmodium berghei.","date":"2026","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/41634752","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["serine/arginine-rich splicing factor 1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6187,"output_tokens":2360,"usd":0.026981,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7685,"output_tokens":3467,"usd":0.06255,"stage2_stop_reason":"end_turn"},"total_usd":0.089531,"stage1_batch_id":"msgbatch_01DbiymDmubkPpYvdbAu5a7V","stage2_batch_id":"msgbatch_012TbrWvMRH129T7PQ4SmvrJ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"PfSR1 (PF3D7_0517300) was identified as a substrate of PfSRPK1 (a novel P. falciparum splicing-related kinase); PfSR1 interacts with RNA, and PfSRPK1 modulates PfSR1's RNA binding activity. Both PfSRPK1 and PfSR1 localize to the nucleus early in parasite development.\",\n      \"method\": \"In vitro kinase assay (substrate identification), RNA-binding assay, nuclear fractionation/localization\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct substrate identification by kinase assay and RNA-binding modulation shown, single lab with two orthogonal methods\",\n      \"pmids\": [\"20870716\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"PfSR1 can mediate RNA splicing in vitro and functions as an alternative splicing factor in mini-gene in vivo systems, similar to mammalian SRSF1. The predicted RS domain of PfSR1 is essential for its localization to the nucleus. Over-expression of pfsr1 influences alternative splicing of P. falciparum genes in vivo, and proper regulation of pfsr1 is required for parasite proliferation in human RBCs.\",\n      \"method\": \"In vitro splicing assay, mini-gene reporter system, PfSR1-myc tagging with live-cell imaging, RS-domain deletion mutagenesis, inducible overexpression with AS analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (in vitro splicing, in vivo mini-gene, mutagenesis of RS domain, inducible overexpression) in a single rigorous study\",\n      \"pmids\": [\"22885299\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PfSR1 localizes adjacent to Nuclear Pore Complex (NPC) clusters in the nucleus of early-stage parasites. RNA immunoprecipitation followed by microarray (RIP-chip) identified endogenous RNA targets of PfSR1; bioinformatic analysis revealed common sequence motifs, and RNA-EMSAs confirmed PfSR1 preferentially binds RNA molecules containing these motifs. PfSR1 regulates not only alternative splicing but also steady-state mRNA levels of transcripts containing these motifs in vivo.\",\n      \"method\": \"Live-cell imaging/fluorescence microscopy, RIP-chip (RNA immunoprecipitation + microarray), RNA-EMSA, inducible overexpression system\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — RIP-chip for endogenous target identification combined with RNA-EMSA validation and in vivo mRNA level changes, multiple orthogonal methods in single study\",\n      \"pmids\": [\"25807998\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"PfSR1 plays an unexpected role in DNA repair in P. falciparum: using an inducible and reversible expression system, PfSR1 was shown to be recruited to foci of DNA damage. Loss of PfSR1 does not impair basal parasite viability but is essential for recovery from DNA-damaging agents and from artemisinin exposure, establishing PfSR1 as required for the DNA damage response.\",\n      \"method\": \"Inducible/reversible knockdown system, immunofluorescence assay for DNA damage foci recruitment, DNA-damaging agent and artemisinin challenge assays\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — inducible reversible system with multiple functional readouts (foci recruitment, chemical challenge with DNA-damaging agents and artemisinin), multiple orthogonal methods in single study\",\n      \"pmids\": [\"34291805\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SR1 (P. berghei ortholog of PF3D7_0517300) is essential for asexual development of malaria parasites. NAB2 and SR1 (but not THO4, NPL3, or GBP2) play essential roles in asexual development of P. berghei.\",\n      \"method\": \"Genetic knockout/knockdown with developmental phenotype assessment in P. berghei\",\n      \"journal\": \"Frontiers in cellular and infection microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic loss-of-function with defined developmental phenotype, single lab\",\n      \"pmids\": [\"34604117\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The N-terminal RRM1 of PfSR1 recognizes RNA with semi-specificity for pyrimidines: a conserved tyrosine on β1 and a glutamate on β4 mediate specific recognition of a cytosine 5' of one or more pyrimidines, while affinity is conferred by insertion of a 3' pyrimidine into a positively charged pocket. RRM1 binds RNA with moderate affinity and retains fast dynamics. The purine preference of PfSR1 was ascertained to reside in the C-terminal pseudo-RRM (RRM2), which binds RNA non-canonically and with greater affinity than RRM1. The two RRMs thus show complementary RNA sequence recognition.\",\n      \"method\": \"NMR solution structure of RRM1–RNA complex, isothermal titration calorimetry (ITC), NMR chemical shift perturbation mapping, site-specific mutagenesis inference from structural data\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structure of protein–RNA complex combined with ITC binding measurements and CSP mapping, single lab but multiple orthogonal structural/biophysical methods\",\n      \"pmids\": [\"30500338\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PbSR1 (P. berghei ortholog of PF3D7_0517300) localizes predominantly to the nucleus but also to the cytoplasm. IP-MS identified PbSR1 interacting partners including nuclear RNA-binding proteins and small nuclear ribonucleoproteins, as well as cytoplasmic rhoptry proteins RhopH1 (Clag3), RhopH2, and RhopH3. Live-cell imaging showed co-localization of PbSR1 and RhopH2 in the cytoplasm of trophozoites and gametocytes but not in mature schizonts or merozoites.\",\n      \"method\": \"Immunoprecipitation coupled to mass spectrometry (IP-MS) of GFP-tagged PbSR1, live-cell fluorescence imaging of co-expressed PbSR1::GFP and RhopH2::mCherry, western blot\",\n      \"journal\": \"Malaria journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal IP-MS with live-cell imaging validation, single lab, two orthogonal methods\",\n      \"pmids\": [\"41634752\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"ANKA\"}]\n    }\n  ],\n  \"current_model\": \"PfSR1/PbSR1 (PF3D7_0517300) is a bona fide SR-family splicing factor that binds RNA through complementary mechanisms of its two RRM domains (RRM1 preferring pyrimidines, RRM2 preferring purines), mediates alternative splicing and regulates steady-state mRNA levels by recognizing specific sequence motifs near Nuclear Pore Complexes, requires its RS domain for nuclear localization, is phosphorylated by PfSRPK1 (which modulates its RNA binding), is essential for asexual parasite proliferation, and additionally plays an unexpected role in DNA repair by being recruited to DNA damage foci and enabling parasite recovery from DNA-damaging agents and artemisinin; in P. berghei it also interacts with rhoptry complex proteins RhopH1/2/3 in the cytoplasm of trophozoites and gametocytes.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0517300 (PfSR1/PbSR1) is a serine/arginine-rich splicing factor that governs RNA processing in malaria parasites, functioning analogously to mammalian SRSF1 by mediating constitutive and alternative splicing and additionally regulating steady-state mRNA levels [#1, #2]. It engages RNA through two RRM domains with complementary sequence preferences: the N-terminal RRM1 recognizes pyrimidines through a conserved tyrosine and glutamate that specify a cytosine 5' of pyrimidines with a 3' pyrimidine inserted into a positively charged pocket, while the C-terminal pseudo-RRM (RRM2) binds purines non-canonically and with higher affinity [#5]. Endogenously, PfSR1 binds transcripts bearing specific sequence motifs and controls both their splicing and abundance in vivo, acting from a nuclear position adjacent to Nuclear Pore Complex clusters [#2]. Its RS domain is required for nuclear localization [#1], and its RNA-binding activity is modulated by phosphorylation by the splicing-related kinase PfSRPK1 [#0]. Proper regulation of the factor is required for asexual proliferation in erythrocytes, and its P. berghei ortholog is essential for asexual development [#1, #4]. Beyond splicing, PfSR1 has an unexpected role in the DNA damage response: it is recruited to DNA damage foci and, while dispensable for basal viability, is required for parasite recovery from DNA-damaging agents and from artemisinin [#3]. In P. berghei, PbSR1 localizes to both nucleus and cytoplasm and, in addition to nuclear RNA-binding partners and small nuclear ribonucleoproteins, co-localizes with the rhoptry proteins RhopH1/2/3 in the cytoplasm of trophozoites and gametocytes [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Establishing that PF3D7_0517300 is an RNA-binding protein and a kinase substrate placed it in a splicing-regulatory context and identified an upstream regulator of its activity.\",\n      \"evidence\": \"In vitro kinase assay, RNA-binding assay, and nuclear fractionation in P. falciparum\",\n      \"pmids\": [\"20870716\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phosphosites on PfSR1 not mapped\", \"Functional consequence of PfSRPK1 phosphorylation on splicing not tested in vivo\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrating splicing activity, RS-domain-dependent nuclear localization, and a proliferation requirement defined PF3D7_0517300 as a bona fide SR splicing factor essential for the parasite.\",\n      \"evidence\": \"In vitro splicing, mini-gene reporters, RS-domain deletion, and inducible overexpression in P. falciparum\",\n      \"pmids\": [\"22885299\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct endogenous splicing targets not yet identified\", \"Mechanism linking splicing defects to proliferation loss unresolved\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identifying endogenous RNA targets and a bound sequence motif showed PF3D7_0517300 regulates both alternative splicing and steady-state mRNA levels from a position at the nuclear periphery.\",\n      \"evidence\": \"RIP-chip, RNA-EMSA, and live-cell imaging near NPC clusters in P. falciparum\",\n      \"pmids\": [\"25807998\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of NPC-adjacent localization not mechanistically dissected\", \"How motif recognition selects splicing vs. mRNA-stability outcomes unknown\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Structural and biophysical dissection of the two RRMs explained how PF3D7_0517300 achieves broad RNA recognition through complementary pyrimidine- and purine-preferring modules.\",\n      \"evidence\": \"NMR structure of RRM1\\u2013RNA complex, ITC, and chemical shift perturbation mapping in P. falciparum\",\n      \"pmids\": [\"30500338\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full-length tandem-RRM RNA complex not resolved\", \"Structural basis of RRM2 non-canonical binding not directly determined\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"An inducible/reversible system revealed a moonlighting role in the DNA damage response, showing PF3D7_0517300 is recruited to damage foci and required for recovery from genotoxic and artemisinin stress despite being dispensable for basal viability.\",\n      \"evidence\": \"Inducible/reversible knockdown, immunofluorescence of damage foci, and DNA-damaging-agent/artemisinin challenge in P. falciparum\",\n      \"pmids\": [\"34291805\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism linking an SR splicing factor to DNA repair unresolved\", \"Whether the repair role depends on RNA binding or splicing activity not determined\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Genetic loss-of-function in P. berghei confirmed the ortholog's essentiality for asexual development, distinguishing it from other mRNA-export/RNA-binding factors that were dispensable.\",\n      \"evidence\": \"Genetic knockout/knockdown with developmental phenotyping in P. berghei\",\n      \"pmids\": [\"34604117\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Stage of developmental arrest not molecularly characterized\", \"Whether essentiality reflects splicing function specifically not addressed\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Interactome and imaging in P. berghei extended the factor's associations beyond nuclear RNA machinery to an unexpected cytoplasmic co-localization with rhoptry proteins in specific developmental stages.\",\n      \"evidence\": \"IP-MS of GFP-tagged PbSR1 and live-cell co-imaging with RhopH2 in P. berghei ANKA\",\n      \"pmids\": [\"41634752\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional significance of the RhopH interaction unknown\", \"Whether cytoplasmic association is direct or indirect not established\", \"Stage-specificity mechanism unexplained\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"ANKA\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PF3D7_0517300 mechanistically bridges its established splicing/mRNA-regulatory function to its DNA damage response role and its cytoplasmic rhoptry-protein association remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No mechanism connecting splicing activity to DNA repair recruitment\", \"Functional role of RhopH co-localization untested\", \"Cross-species reconciliation of nuclear vs. cytoplasmic roles absent\"],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 2, 5]},\n      {\"term_id\": \"GO:0008380\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0003729\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1, 6]},\n      {\"term_id\": \"GO:0044615\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005737\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0000380\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0006281\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0006974\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PfSRPK1 (kinase, phosphorylates PfSR1; P. falciparum)\",\n      \"RhopH1/Clag3 (P. berghei, cytoplasmic co-localization)\",\n      \"RhopH2 (P. berghei, cytoplasmic co-localization)\",\n      \"RhopH3 (P. berghei)\",\n      \"nuclear RNA-binding proteins and small nuclear ribonucleoproteins (P. berghei IP-MS)\"\n    ],\n    \"other_free_text\": [\n      \"Two-RRM architecture with complementary RNA sequence preference: RRM1 pyrimidine-preferring, RRM2 (pseudo-RRM) purine-preferring [#5]\",\n      \"RS domain required for nuclear localization [#1]\",\n      \"Regulates both alternative splicing and steady-state mRNA levels of motif-containing transcripts [#2]\",\n      \"Essential for asexual proliferation in P. falciparum and asexual development in P. berghei [#1, #4]\",\n      \"Required for recovery from DNA-damaging agents and artemisinin; recruited to DNA damage foci [#3]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0517300","name":null,"product":"serine/arginine-rich splicing factor 1","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1232100","name":null,"product":"serine/arginine-rich splicing factor 1, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1016000","name":null,"product":"serine/arginine-rich splicing factor 1, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}