{"gene":"PF3D7_1123900","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2012,"finding":"SNU13 (PF3D7_1123900) was detected as a nuclear protein in P. falciparum by high-accuracy mass spectrometry-based nuclear proteomics, placing it in the experimentally determined core nuclear proteome. Network analysis of the nuclear proteome identified SNU13 as a central node connecting clusters assigned to mRNA splicing/processing, the nucleolus, and translation initiation.","method":"High-accuracy mass spectrometry of nuclear fractions; STRING-based protein-protein interaction network analysis","journal":"Genome biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — nuclear fractionation + MS localization in a single study; network placement is bioinformatic, not direct functional experiment","pmids":["23181666"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"finding":"SNU13 (PF3D7_1123900) was identified as an interactor of PfSAMS (S-adenosylmethionine synthetase) in a proximity-dependent biotin identification (TurboID/BioID) screen, and network analysis placed it as the intermediary connecting the spliceosome protein cluster to the translation initiation factor cluster in P. falciparum blood-stage parasites.","method":"Proximity-dependent biotin identification (BioID/TurboID) coupled to mass spectrometry; STRING interaction network analysis","journal":"Microorganisms","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single proximity-labeling experiment in one lab; network placement is bioinformatic inference","pmids":["35889137"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"finding":"SNU13 (PF3D7_1123900) was identified as an interactor of PfSET10 by TurboID coupled with mass spectrometry in P. falciparum blood-stage parasites; network analysis placed SNU13 as a central protein connecting clusters related to mRNA processing, ribosomes/translation, and spliceosome function within the PfSET10 interaction network.","method":"TurboID proximity labeling coupled to mass spectrometry; STRING-based protein-protein interaction network analysis","journal":"mSphere","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single proximity-labeling experiment in one lab; network role is bioinformatic inference only","pmids":["39445823"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2009,"finding":"A P. falciparum homologue of SNU13 was identified bioinformatically as a component of the box C/D snoRNP complex (alongside fibrillarin, Nop56, and Nop58), implicating it in rRNA 2'-O-ribose methylation and ribosome biogenesis in malaria parasites.","method":"Computational homology search (PSI-BLAST) across Plasmodium genomes","journal":"BMC genomics","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational prediction only, no direct biochemical experiment performed on the Plasmodium protein","pmids":["19200392"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1123900 (SNU13) is a nuclear protein in P. falciparum, detected in the core nuclear proteome by mass spectrometry, that occupies a central network position linking spliceosomal/mRNA-processing complexes, the nucleolus, and translation initiation factors, and has been identified as a proximity interactor of both PfSAMS and PfSET10; it is also predicted by homology to be a component of the box C/D snoRNP, but no direct biochemical or functional experiment has been performed on the P. falciparum protein itself."},"narrative":{"mechanistic_narrative":"PF3D7_1123900 (SNU13) is a nuclear protein of Plasmodium falciparum identified in the experimentally determined core nuclear proteome by high-accuracy mass spectrometry, where network analysis positioned it as a central node bridging clusters assigned to mRNA splicing/processing, the nucleolus, and translation initiation [PMID:23181666]. Beyond this localization and network placement, no direct biochemical or functional experiment has been performed on the P. falciparum protein itself; its assignment as a box C/D snoRNP component (with fibrillarin, Nop56, and Nop58) rests on computational homology rather than experiment [PMID:19200392], and its detection as a proximity interactor of PfSAMS and PfSET10 comes from single proximity-labeling screens with bioinformatic network interpretation [PMID:35889137, PMID:39445823]. The corpus therefore establishes SNU13 as a nuclear, network-central protein linked by inference to spliceosomal, ribosome-biogenesis, and translation-associated machinery, but no molecular activity of PF3D7_1123900 has been directly demonstrated.","teleology":[{"year":2009,"claim":"To ask whether malaria parasites possess the conserved rRNA-modification machinery, a homology search tested whether a SNU13 homologue exists as part of the box C/D snoRNP.","evidence":"Computational PSI-BLAST homology search across Plasmodium genomes","pmids":["19200392"],"confidence":"Low","gaps":["Purely computational prediction with no biochemical validation on the Plasmodium protein","snoRNP membership and rRNA 2'-O-methylation role not experimentally confirmed for PF3D7_1123900","No demonstration of physical association with fibrillarin, Nop56, or Nop58 in the parasite"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"claim":"To establish where PF3D7_1123900 acts, nuclear proteomics placed it experimentally in the core nuclear proteome and network analysis identified it as a hub connecting splicing/processing, nucleolar, and translation-initiation clusters.","evidence":"High-accuracy mass spectrometry of nuclear fractions with STRING network analysis in P. falciparum","pmids":["23181666"],"confidence":"Medium","gaps":["Network centrality is bioinformatic inference, not a functional assay","No direct molecular activity assigned to the protein","Does not distinguish which of the linked processes SNU13 directly participates in"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2022,"claim":"A proximity-labeling screen around PfSAMS tested SNU13's local environment and placed it as an intermediary linking the spliceosome cluster to translation initiation factors.","evidence":"BioID/TurboID proximity labeling coupled to mass spectrometry with STRING network analysis in blood-stage parasites","pmids":["35889137"],"confidence":"Low","gaps":["Single proximity-labeling experiment; proximity does not establish a direct or functional interaction","Network role is bioinformatic inference","No reciprocal validation of the PfSAMS association"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"claim":"A TurboID screen around PfSET10 again recovered SNU13, reinforcing its network position bridging mRNA processing, ribosomes/translation, and spliceosome clusters.","evidence":"TurboID proximity labeling coupled to mass spectrometry with STRING network analysis in blood-stage parasites","pmids":["39445823"],"confidence":"Low","gaps":["Single proximity-labeling experiment in one lab","Network centrality is bioinformatic, not functional","Does not establish a direct SNU13–PfSET10 interaction or a shared pathway"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"No direct biochemical or functional experiment has defined the molecular activity, RNA/protein partners, or in vivo role of PF3D7_1123900 itself; whether it functions in box C/D snoRNP-mediated rRNA methylation, spliceosome assembly, or translation remains experimentally unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No knockout, knockdown, or complementation phenotype for PF3D7_1123900","No demonstrated RNA-binding or snoRNP assembly activity in the parasite","No structural or reconstitution data on the P. falciparum protein"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["box C/D snoRNP (predicted by homology only) [#3]"],"partners":["PFSAMS (PROXIMITY INTERACTOR) [#1]","PFSET10 (PROXIMITY INTERACTOR) [#2]"],"other_free_text":["Detected in the experimentally determined core nuclear proteome of P. falciparum by mass spectrometry [#0].","Consistently placed by network analysis as a central node bridging mRNA splicing/processing, nucleolar, ribosome/translation, and translation-initiation clusters, but this centrality is bioinformatic inference, not a functional assay [#0, #1, #2].","No direct biochemical or functional experiment has been performed on PF3D7_1123900 itself; all mechanistic assignments rest on homology or network inference."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"23181666","id":"PMC_23181666","title":"Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum.","date":"2012","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/23181666","citation_count":120,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39445823","id":"","title":"The Plasmodium falciparum histone methyltransferase SET10 participates in a chromatin modulation network crucial for intraerythrocytic development.","date":"2024","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/39445823","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SNU13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35889137","id":"","title":"Plasmodium falciparum S-Adenosylmethionine Synthetase Is Essential for Parasite Survival through a Complex Interaction Network with Cytoplasmic and Nuclear Proteins.","date":"2022","source":"Microorganisms","url":"https://pubmed.ncbi.nlm.nih.gov/35889137","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SNU13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"36631250","id":"","title":"Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome.","date":"2023","source":"Molecular biology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/36631250","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SNU13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"36737103","id":"","title":"Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes.","date":"2023","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/36737103","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SNU13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19200392","id":"","title":"Analysis of small nucleolar RNAs reveals unique genetic features in malaria parasites.","date":"2009","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/19200392","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SNU13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35648437","id":"","title":"Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/35648437","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SNU13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24214024","id":"","title":"Origin and evolution of the eukaryotic SSU processome revealed by a comprehensive genomic analysis and implications for the origin of the nucleolus.","date":"2013","source":"Genome biology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/24214024","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SNU13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"32301288","id":"","title":"Naturally occurring modified ribonucleosides.","date":"2020","source":"Wiley interdisciplinary reviews. RNA","url":"https://pubmed.ncbi.nlm.nih.gov/32301288","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SNU13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25968466","id":"","title":"Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes.","date":"2015","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/25968466","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SNU13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14191,"output_tokens":1152,"usd":0.029927,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5990,"output_tokens":2231,"usd":0.042862,"stage2_stop_reason":"end_turn"},"total_usd":0.072789,"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\": 2012,\n      \"finding\": \"SNU13 (PF3D7_1123900) was detected as a nuclear protein in P. falciparum by high-accuracy mass spectrometry-based nuclear proteomics, placing it in the experimentally determined core nuclear proteome. Network analysis of the nuclear proteome identified SNU13 as a central node connecting clusters assigned to mRNA splicing/processing, the nucleolus, and translation initiation.\",\n      \"method\": \"High-accuracy mass spectrometry of nuclear fractions; STRING-based protein-protein interaction network analysis\",\n      \"journal\": \"Genome biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — nuclear fractionation + MS localization in a single study; network placement is bioinformatic, not direct functional experiment\",\n      \"pmids\": [\"23181666\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SNU13 (PF3D7_1123900) was identified as an interactor of PfSAMS (S-adenosylmethionine synthetase) in a proximity-dependent biotin identification (TurboID/BioID) screen, and network analysis placed it as the intermediary connecting the spliceosome protein cluster to the translation initiation factor cluster in P. falciparum blood-stage parasites.\",\n      \"method\": \"Proximity-dependent biotin identification (BioID/TurboID) coupled to mass spectrometry; STRING interaction network analysis\",\n      \"journal\": \"Microorganisms\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single proximity-labeling experiment in one lab; network placement is bioinformatic inference\",\n      \"pmids\": [\"35889137\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SNU13 (PF3D7_1123900) was identified as an interactor of PfSET10 by TurboID coupled with mass spectrometry in P. falciparum blood-stage parasites; network analysis placed SNU13 as a central protein connecting clusters related to mRNA processing, ribosomes/translation, and spliceosome function within the PfSET10 interaction network.\",\n      \"method\": \"TurboID proximity labeling coupled to mass spectrometry; STRING-based protein-protein interaction network analysis\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single proximity-labeling experiment in one lab; network role is bioinformatic inference only\",\n      \"pmids\": [\"39445823\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"A P. falciparum homologue of SNU13 was identified bioinformatically as a component of the box C/D snoRNP complex (alongside fibrillarin, Nop56, and Nop58), implicating it in rRNA 2'-O-ribose methylation and ribosome biogenesis in malaria parasites.\",\n      \"method\": \"Computational homology search (PSI-BLAST) across Plasmodium genomes\",\n      \"journal\": \"BMC genomics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational prediction only, no direct biochemical experiment performed on the Plasmodium protein\",\n      \"pmids\": [\"19200392\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1123900 (SNU13) is a nuclear protein in P. falciparum, detected in the core nuclear proteome by mass spectrometry, that occupies a central network position linking spliceosomal/mRNA-processing complexes, the nucleolus, and translation initiation factors, and has been identified as a proximity interactor of both PfSAMS and PfSET10; it is also predicted by homology to be a component of the box C/D snoRNP, but no direct biochemical or functional experiment has been performed on the P. falciparum protein itself.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1123900 (SNU13) is a nuclear protein of Plasmodium falciparum identified in the experimentally determined core nuclear proteome by high-accuracy mass spectrometry, where network analysis positioned it as a central node bridging clusters assigned to mRNA splicing/processing, the nucleolus, and translation initiation [#0]. Beyond this localization and network placement, no direct biochemical or functional experiment has been performed on the P. falciparum protein itself; its assignment as a box C/D snoRNP component (with fibrillarin, Nop56, and Nop58) rests on computational homology rather than experiment [#3], and its detection as a proximity interactor of PfSAMS and PfSET10 comes from single proximity-labeling screens with bioinformatic network interpretation [#1, #2]. The corpus therefore establishes SNU13 as a nuclear, network-central protein linked by inference to spliceosomal, ribosome-biogenesis, and translation-associated machinery, but no molecular activity of PF3D7_1123900 has been directly demonstrated.\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"To ask whether malaria parasites possess the conserved rRNA-modification machinery, a homology search tested whether a SNU13 homologue exists as part of the box C/D snoRNP.\",\n      \"evidence\": \"Computational PSI-BLAST homology search across Plasmodium genomes\",\n      \"pmids\": [\"19200392\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Purely computational prediction with no biochemical validation on the Plasmodium protein\", \"snoRNP membership and rRNA 2'-O-methylation role not experimentally confirmed for PF3D7_1123900\", \"No demonstration of physical association with fibrillarin, Nop56, or Nop58 in the parasite\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"To establish where PF3D7_1123900 acts, nuclear proteomics placed it experimentally in the core nuclear proteome and network analysis identified it as a hub connecting splicing/processing, nucleolar, and translation-initiation clusters.\",\n      \"evidence\": \"High-accuracy mass spectrometry of nuclear fractions with STRING network analysis in P. falciparum\",\n      \"pmids\": [\"23181666\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Network centrality is bioinformatic inference, not a functional assay\", \"No direct molecular activity assigned to the protein\", \"Does not distinguish which of the linked processes SNU13 directly participates in\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"A proximity-labeling screen around PfSAMS tested SNU13's local environment and placed it as an intermediary linking the spliceosome cluster to translation initiation factors.\",\n      \"evidence\": \"BioID/TurboID proximity labeling coupled to mass spectrometry with STRING network analysis in blood-stage parasites\",\n      \"pmids\": [\"35889137\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single proximity-labeling experiment; proximity does not establish a direct or functional interaction\", \"Network role is bioinformatic inference\", \"No reciprocal validation of the PfSAMS association\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A TurboID screen around PfSET10 again recovered SNU13, reinforcing its network position bridging mRNA processing, ribosomes/translation, and spliceosome clusters.\",\n      \"evidence\": \"TurboID proximity labeling coupled to mass spectrometry with STRING network analysis in blood-stage parasites\",\n      \"pmids\": [\"39445823\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single proximity-labeling experiment in one lab\", \"Network centrality is bioinformatic, not functional\", \"Does not establish a direct SNU13–PfSET10 interaction or a shared pathway\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"No direct biochemical or functional experiment has defined the molecular activity, RNA/protein partners, or in vivo role of PF3D7_1123900 itself; whether it functions in box C/D snoRNP-mediated rRNA methylation, spliceosome assembly, or translation remains experimentally unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No knockout, knockdown, or complementation phenotype for PF3D7_1123900\", \"No demonstrated RNA-binding or snoRNP assembly activity in the parasite\", \"No structural or reconstitution data on the P. falciparum protein\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006364\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0000398\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"complexes\": [\"box C/D snoRNP (predicted by homology only) [#3]\"],\n    \"partners\": [\"PfSAMS (proximity interactor) [#1]\", \"PfSET10 (proximity interactor) [#2]\"],\n    \"other_free_text\": [\n      \"Detected in the experimentally determined core nuclear proteome of P. falciparum by mass spectrometry [#0].\",\n      \"Consistently placed by network analysis as a central node bridging mRNA splicing/processing, nucleolar, ribosome/translation, and translation-initiation clusters, but this centrality is bioinformatic inference, not a functional assay [#0, #1, #2].\",\n      \"No direct biochemical or functional experiment has been performed on PF3D7_1123900 itself; all mechanistic assignments rest on homology or network inference.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1123900","name":null,"product":"13 kDa ribonucleoprotein-associated protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0924400","name":null,"product":"13 kDa ribonucleoprotein-associated protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0921700","name":null,"product":"13 kDa ribonucleoprotein-associated protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"SNU13","evaluation":null}