{"gene":"PF3D7_0520300","run_date":"2026-09-08T19:44:17","timeline":{"discoveries":[{"year":2024,"finding":"LSM2 (PF3D7_0520300) was identified as a component of PfDOZI-associated processing body (PB)-like mRNPs in P. falciparum schizonts, co-immunoprecipitating with PfDOZI alongside other mRNA decay-related proteins (DCP2, DCP1, LSm1-4, LSm7, NOT1, CAF1, CAF40); LSM2 was relatively more abundant in schizont-stage PfDOZI complexes than core stress granule components, consistent with a role in mRNA decay.","method":"GFP-trap immunoprecipitation of PfDOZI::GFP followed by mass spectrometry-based protein identification","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single Co-IP/MS experiment identifying LSM2 as a co-purifying protein; no direct functional validation of LSM2 itself, single lab","pmids":["38702310"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"finding":"LSM2 (PF3D7_0520300) was detected in the experimentally determined core nuclear proteome of P. falciparum, indicating nuclear localization of this protein.","method":"High-accuracy mass spectrometry of isolated nuclear fractions combined with bioinformatic analysis; validated with transgenic cell lines","journal":"Genome biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — large-scale proteomics inventory; LSM2 is one of hundreds of proteins detected; no specific functional experiment performed on this protein","pmids":["23181666"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"In P. falciparum, LSM2 (PF3D7_0520300) has been detected in the nuclear proteome and identified as a component of PfDOZI-associated processing body-like mRNPs in schizonts, where it co-purifies with mRNA decay machinery (decapping enzymes and deadenylase complex), suggesting membership in an mRNA decay complex, but no direct functional experiments have been performed on LSM2 itself."},"narrative":{"mechanistic_narrative":"LSM2 (PF3D7_0520300) is an Sm-like protein of P. falciparum that has been placed within the mRNA decay machinery through its co-purification with PfDOZI-associated processing body (PB)-like mRNPs in schizonts [PMID:38702310]. In this context LSM2 co-immunoprecipitates with PfDOZI alongside decapping enzymes (DCP2, DCP1), other LSm proteins (LSm1-4, LSm7), and the deadenylase/CCR4-NOT-associated components NOT1, CAF1 and CAF40, and is relatively more abundant in schizont-stage PfDOZI complexes than core stress granule components, consistent with a role in mRNA decay [PMID:38702310]. LSM2 has also been detected in the experimentally determined core nuclear proteome of P. falciparum [PMID:23181666]. Beyond this membership in the PfDOZI mRNP and its nuclear detection, no direct functional experiments have been performed on LSM2 itself in the available corpus.","teleology":[{"year":2012,"claim":"Establishing where LSM2 resides was the first step toward assigning it a cellular role; detection in the isolated nuclear fraction placed the protein in the nucleus.","evidence":"high-accuracy mass spectrometry of isolated nuclear fractions with bioinformatic analysis, validated with transgenic lines, in P. falciparum","pmids":["23181666"],"confidence":"Low","gaps":["Large-scale proteomic inventory with no functional experiment on LSM2 specifically","Does not resolve subnuclear localization or associated complexes","Nuclear detection is not reconciled with the later cytoplasmic mRNP association"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"claim":"Whether LSM2 participates in mRNA metabolism was addressed by showing it is a component of PfDOZI-associated PB-like mRNPs enriched for decay machinery, implicating it in mRNA decay rather than storage.","evidence":"GFP-trap immunoprecipitation of PfDOZI::GFP followed by mass spectrometry in P. falciparum schizonts","pmids":["38702310"],"confidence":"Medium","gaps":["Single Co-IP/MS experiment with no reciprocal pull-down or direct functional validation of LSM2","Does not establish which RNAs or complex subunits LSM2 directly contacts","No knockout, knockdown, or biochemical reconstitution of LSM2 function"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown whether LSM2 has any function beyond its membership in the PfDOZI mRNP, and no direct biochemical or genetic role has been defined for the protein.","evidence":"no direct functional study of LSM2 in the available corpus","pmids":[],"confidence":"Low","gaps":["No genetic ablation or phenotype for LSM2","No demonstration of direct RNA binding or Sm-like ring assembly by LSM2","No resolution of how nuclear detection relates to cytoplasmic mRNP association"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["PfDOZI-associated processing body (PB)-like mRNP"],"partners":["PFDOZI","DCP2","DCP1","LSM1-4","LSM7","NOT1","CAF1","CAF40"],"other_free_text":["Detected in the experimentally determined core nuclear proteome of P. falciparum [#1].","Relatively more abundant in schizont-stage PfDOZI complexes than core stress granule components, consistent with mRNA decay rather than storage [#0].","No direct functional experiments (knockout, RNA-binding assay, or reconstitution) have been performed on LSM2 itself in the available corpus."]}},"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":"21245033","id":"PMC_21245033","title":"RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts.","date":"2011","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/21245033","citation_count":108,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38702310","id":"","title":"The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38702310","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["LSM2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19282982","id":"","title":"Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome.","date":"2009","source":"PLoS computational biology","url":"https://pubmed.ncbi.nlm.nih.gov/19282982","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["LSM2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5952,"output_tokens":666,"usd":0.013923,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5277,"output_tokens":1639,"usd":0.03368,"stage2_stop_reason":"end_turn"},"total_usd":0.047603,"stage1_batch_id":"msgbatch_01SRp5hyRc82zNjddxyCCXGk","stage2_batch_id":"msgbatch_01K3BTmBazRo3pRrMvyaPMTY","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2024,\n      \"finding\": \"LSM2 (PF3D7_0520300) was identified as a component of PfDOZI-associated processing body (PB)-like mRNPs in P. falciparum schizonts, co-immunoprecipitating with PfDOZI alongside other mRNA decay-related proteins (DCP2, DCP1, LSm1-4, LSm7, NOT1, CAF1, CAF40); LSM2 was relatively more abundant in schizont-stage PfDOZI complexes than core stress granule components, consistent with a role in mRNA decay.\",\n      \"method\": \"GFP-trap immunoprecipitation of PfDOZI::GFP followed by mass spectrometry-based protein identification\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/MS experiment identifying LSM2 as a co-purifying protein; no direct functional validation of LSM2 itself, single lab\",\n      \"pmids\": [\"38702310\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"LSM2 (PF3D7_0520300) was detected in the experimentally determined core nuclear proteome of P. falciparum, indicating nuclear localization of this protein.\",\n      \"method\": \"High-accuracy mass spectrometry of isolated nuclear fractions combined with bioinformatic analysis; validated with transgenic cell lines\",\n      \"journal\": \"Genome biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — large-scale proteomics inventory; LSM2 is one of hundreds of proteins detected; no specific functional experiment performed on this protein\",\n      \"pmids\": [\"23181666\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"In P. falciparum, LSM2 (PF3D7_0520300) has been detected in the nuclear proteome and identified as a component of PfDOZI-associated processing body-like mRNPs in schizonts, where it co-purifies with mRNA decay machinery (decapping enzymes and deadenylase complex), suggesting membership in an mRNA decay complex, but no direct functional experiments have been performed on LSM2 itself.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LSM2 (PF3D7_0520300) is an Sm-like protein of P. falciparum that has been placed within the mRNA decay machinery through its co-purification with PfDOZI-associated processing body (PB)-like mRNPs in schizonts [#0]. In this context LSM2 co-immunoprecipitates with PfDOZI alongside decapping enzymes (DCP2, DCP1), other LSm proteins (LSm1-4, LSm7), and the deadenylase/CCR4-NOT-associated components NOT1, CAF1 and CAF40, and is relatively more abundant in schizont-stage PfDOZI complexes than core stress granule components, consistent with a role in mRNA decay [#0]. LSM2 has also been detected in the experimentally determined core nuclear proteome of P. falciparum [#1]. Beyond this membership in the PfDOZI mRNP and its nuclear detection, no direct functional experiments have been performed on LSM2 itself in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Establishing where LSM2 resides was the first step toward assigning it a cellular role; detection in the isolated nuclear fraction placed the protein in the nucleus.\",\n      \"evidence\": \"high-accuracy mass spectrometry of isolated nuclear fractions with bioinformatic analysis, validated with transgenic lines, in P. falciparum\",\n      \"pmids\": [\"23181666\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Large-scale proteomic inventory with no functional experiment on LSM2 specifically\",\n        \"Does not resolve subnuclear localization or associated complexes\",\n        \"Nuclear detection is not reconciled with the later cytoplasmic mRNP association\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Whether LSM2 participates in mRNA metabolism was addressed by showing it is a component of PfDOZI-associated PB-like mRNPs enriched for decay machinery, implicating it in mRNA decay rather than storage.\",\n      \"evidence\": \"GFP-trap immunoprecipitation of PfDOZI::GFP followed by mass spectrometry in P. falciparum schizonts\",\n      \"pmids\": [\"38702310\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single Co-IP/MS experiment with no reciprocal pull-down or direct functional validation of LSM2\",\n        \"Does not establish which RNAs or complex subunits LSM2 directly contacts\",\n        \"No knockout, knockdown, or biochemical reconstitution of LSM2 function\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether LSM2 has any function beyond its membership in the PfDOZI mRNP, and no direct biochemical or genetic role has been defined for the protein.\",\n      \"evidence\": \"no direct functional study of LSM2 in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No genetic ablation or phenotype for LSM2\",\n        \"No demonstration of direct RNA binding or Sm-like ring assembly by LSM2\",\n        \"No resolution of how nuclear detection relates to cytoplasmic mRNP association\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006402\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\n      \"PfDOZI-associated processing body (PB)-like mRNP\"\n    ],\n    \"partners\": [\n      \"PfDOZI\",\n      \"DCP2\",\n      \"DCP1\",\n      \"LSm1-4\",\n      \"LSm7\",\n      \"NOT1\",\n      \"CAF1\",\n      \"CAF40\"\n    ],\n    \"other_free_text\": [\n      \"Detected in the experimentally determined core nuclear proteome of P. falciparum [#1].\",\n      \"Relatively more abundant in schizont-stage PfDOZI complexes than core stress granule components, consistent with mRNA decay rather than storage [#0].\",\n      \"No direct functional experiments (knockout, RNA-binding assay, or reconstitution) have been performed on LSM2 itself in the available corpus.\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_0520300","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 1 of 2 cited papers name other catalogue genes (PF3D7_0315100, PF3D7_0320800, PF3D7_0507600). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0520300","name":null,"product":"U6 snRNA-associated Sm-like protein LSm2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"LSM2","evaluation":null}