{"gene":"PF3D7_0925800","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2023,"finding":"PfUPF2 (PF3D7_0925800) localizes to puncta within the P. falciparum parasite cytoplasm, as determined by epitope-tagging and microscopy following CRISPR-Cas9 editing.","method":"CRISPR-Cas9 epitope-tagging, fluorescence microscopy","journal":"mSphere","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with epitope-tagging and imaging, single lab but with CRISPR-based tagging and functional context","pmids":["37366629"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"finding":"PfUPF2 (PF3D7_0925800) physically interacts with PfUPF1 (PF3D7_1005500) and other mRNA-binding proteins in P. falciparum, establishing its membership in an NMD complex.","method":"Co-immunoprecipitation / protein interaction assay following CRISPR-Cas9 epitope-tagging","journal":"mSphere","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP from one lab, but epitope-tag approach is clean and interaction with UPF1 is consistent with conserved NMD complex biology","pmids":["37366629"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"finding":"Disruption of PfUPF2 (PF3D7_0925800) by CRISPR-Cas9 does not result in degradation of nonsense transcripts and does not impair parasite growth ex vivo, demonstrating that the NMD pathway involving PfUPF2 is non-essential for mRNA quality control and parasite viability in asexual blood stages.","method":"CRISPR-Cas9 knockout, RNA-seq analysis of nonsense transcript abundance, parasite growth assay","journal":"mSphere","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean CRISPR knockout with RNA-seq readout and growth phenotyping, multiple orthogonal methods in a single rigorous study","pmids":["37366629"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2026,"finding":"Disruption of the NMD pathway (including loss of UPF2/PF3D7_0925800 function) stabilizes the var2csa transcript in P. falciparum 'switcher' lines, indicating that NMD directly degrades the var2csa mRNA when it is not fully translated (due to an upstream ORF in the 5'-UTR), thereby promoting transcriptional activation of an alternative var gene.","method":"NMD pathway disruption (knockout), RNA-seq, var2csa transcript stability measurement, uORF start-codon mutagenesis","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional consequence of NMD loss on var2csa mRNA stability shown with multiple methods in one lab; UPF2 contribution inferred from pathway disruption rather than UPF2-specific experiment","pmids":["41851501"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"In P. falciparum, PfUPF2 (PF3D7_0925800) localizes to cytoplasmic puncta and forms a complex with PfUPF1 and other mRNA-binding proteins (including PfAlba4); although the NMD machinery it belongs to is expressed and intact, it is non-essential for bulk nonsense-transcript degradation and asexual blood-stage growth, yet the NMD pathway does appear to specifically degrade the var2csa mRNA via an upstream ORF mechanism to regulate var gene switching."},"narrative":{"mechanistic_narrative":"PF3D7_0925800 (UPF2) is a component of the nonsense-mediated mRNA decay (NMD) machinery in Plasmodium falciparum, localizing to discrete puncta within the parasite cytoplasm [PMID:37366629] and physically associating with PfUPF1 and other mRNA-binding proteins, establishing its membership in an NMD complex [PMID:37366629]. Despite the machinery being expressed and intact, CRISPR-Cas9 disruption of PF3D7_0925800 does not lead to accumulation or degradation of bulk nonsense transcripts and does not impair asexual blood-stage growth, indicating that UPF2-dependent NMD is non-essential for global mRNA quality control and parasite viability under these conditions [PMID:37366629]. However, loss of NMD pathway function, including UPF2, stabilizes the var2csa transcript in 'switcher' lines, consistent with NMD selectively degrading incompletely translated var2csa mRNA via an upstream ORF in its 5'-UTR to promote activation of an alternative var gene [PMID:41851501]. Beyond these findings, the biochemical mechanism by which PF3D7_0925800 recognizes or licenses target transcripts has not been characterized in the available corpus.","teleology":[{"year":2023,"claim":"It was unknown where UPF2 acts in the parasite; epitope-tagging placed the protein in cytoplasmic puncta, giving a subcellular context for its function.","evidence":"CRISPR-Cas9 epitope-tagging and fluorescence microscopy in P. falciparum","pmids":["37366629"],"confidence":"Medium","gaps":["Nature and composition of the puncta not defined","Whether localization changes across the parasite life cycle not addressed"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"claim":"Whether PF3D7_0925800 assembles into a functional NMD complex was unresolved; Co-IP demonstrated physical interaction with PfUPF1 and other mRNA-binding proteins, establishing its membership in an NMD complex.","evidence":"Co-immunoprecipitation following CRISPR-Cas9 epitope-tagging in P. falciparum","pmids":["37366629"],"confidence":"Medium","gaps":["Single Co-IP without reciprocal validation","Stoichiometry and full composition of the complex not defined","Direct versus bridged interaction with UPF1 not distinguished"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"claim":"The functional requirement for UPF2-dependent NMD was untested; knockout showed no bulk nonsense-transcript degradation and no growth defect, establishing that this pathway is dispensable for global mRNA quality control and asexual viability.","evidence":"CRISPR-Cas9 knockout with RNA-seq of nonsense transcript abundance and growth assay in P. falciparum","pmids":["37366629"],"confidence":"High","gaps":["Whether UPF2 has non-canonical or stage-specific roles not addressed","Whether a subset of transcripts requires UPF2 not resolved by bulk RNA-seq"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2026,"claim":"It was unclear whether NMD had any specific substrate given its dispensability for bulk decay; disruption of the pathway stabilized var2csa mRNA, showing NMD selectively degrades this uORF-containing transcript to regulate var gene switching.","evidence":"NMD pathway knockout, RNA-seq, var2csa transcript stability measurement and uORF start-codon mutagenesis in P. falciparum switcher lines","pmids":["41851501"],"confidence":"Medium","gaps":["UPF2 contribution inferred from pathway disruption rather than a UPF2-specific experiment","Direct binding of UPF2 to var2csa mRNA not demonstrated","Generality across other var genes not established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The molecular mechanism by which PF3D7_0925800 recognizes uORF-containing or incompletely translated transcripts and licenses their decay remains unknown.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No direct RNA-binding or substrate-recognition experiment for UPF2","No structural model of the parasite NMD complex","Mechanism linking uORF translation to UPF2-dependent decay unresolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["NMD complex containing PfUPF1 (PF3D7_1005500) and other mRNA-binding proteins"],"partners":["PFUPF1 (PF3D7_1005500)"],"other_free_text":["PF3D7_0925800 disruption does not degrade bulk nonsense transcripts and does not impair asexual blood-stage growth [#2]","NMD pathway disruption stabilizes the uORF-containing var2csa transcript, linking the pathway to var gene switching [#3]","UPF2-specific contribution to var2csa regulation is inferred from pathway disruption rather than a UPF2-specific experiment [#3]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"37366629","id":"PMC_37366629","title":"Nonsense-mediated decay machinery in Plasmodium falciparum is inefficient and non-essential.","date":"2023","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/37366629","citation_count":10,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfUPF2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41851501","id":"","title":"Mechanistic insights into coordinated var transcriptional switching in malaria parasites.","date":"2026","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/41851501","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["UPF2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39868986","id":"","title":"Ectopic overexpression of Plasmodium falciparum DNA-/RNA-binding Alba proteins misregulates virulence gene homeostasis during asexual blood development.","date":"2025","source":"Microbiology spectrum","url":"https://pubmed.ncbi.nlm.nih.gov/39868986","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["UPF2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"36093191","id":"","title":"Single-cell RNA profiling of Plasmodium vivax-infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets.","date":"2022","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/36093191","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["UPF2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"21245033","id":"","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":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["UPF2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7713,"output_tokens":1160,"usd":0.020269,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5975,"output_tokens":2200,"usd":0.042438,"stage2_stop_reason":"end_turn"},"total_usd":0.062707,"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\": \"PfUPF2 (PF3D7_0925800) localizes to puncta within the P. falciparum parasite cytoplasm, as determined by epitope-tagging and microscopy following CRISPR-Cas9 editing.\",\n      \"method\": \"CRISPR-Cas9 epitope-tagging, fluorescence microscopy\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with epitope-tagging and imaging, single lab but with CRISPR-based tagging and functional context\",\n      \"pmids\": [\"37366629\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PfUPF2 (PF3D7_0925800) physically interacts with PfUPF1 (PF3D7_1005500) and other mRNA-binding proteins in P. falciparum, establishing its membership in an NMD complex.\",\n      \"method\": \"Co-immunoprecipitation / protein interaction assay following CRISPR-Cas9 epitope-tagging\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP from one lab, but epitope-tag approach is clean and interaction with UPF1 is consistent with conserved NMD complex biology\",\n      \"pmids\": [\"37366629\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Disruption of PfUPF2 (PF3D7_0925800) by CRISPR-Cas9 does not result in degradation of nonsense transcripts and does not impair parasite growth ex vivo, demonstrating that the NMD pathway involving PfUPF2 is non-essential for mRNA quality control and parasite viability in asexual blood stages.\",\n      \"method\": \"CRISPR-Cas9 knockout, RNA-seq analysis of nonsense transcript abundance, parasite growth assay\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean CRISPR knockout with RNA-seq readout and growth phenotyping, multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"37366629\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Disruption of the NMD pathway (including loss of UPF2/PF3D7_0925800 function) stabilizes the var2csa transcript in P. falciparum 'switcher' lines, indicating that NMD directly degrades the var2csa mRNA when it is not fully translated (due to an upstream ORF in the 5'-UTR), thereby promoting transcriptional activation of an alternative var gene.\",\n      \"method\": \"NMD pathway disruption (knockout), RNA-seq, var2csa transcript stability measurement, uORF start-codon mutagenesis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional consequence of NMD loss on var2csa mRNA stability shown with multiple methods in one lab; UPF2 contribution inferred from pathway disruption rather than UPF2-specific experiment\",\n      \"pmids\": [\"41851501\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"In P. falciparum, PfUPF2 (PF3D7_0925800) localizes to cytoplasmic puncta and forms a complex with PfUPF1 and other mRNA-binding proteins (including PfAlba4); although the NMD machinery it belongs to is expressed and intact, it is non-essential for bulk nonsense-transcript degradation and asexual blood-stage growth, yet the NMD pathway does appear to specifically degrade the var2csa mRNA via an upstream ORF mechanism to regulate var gene switching.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0925800 (UPF2) is a component of the nonsense-mediated mRNA decay (NMD) machinery in Plasmodium falciparum, localizing to discrete puncta within the parasite cytoplasm [#0] and physically associating with PfUPF1 and other mRNA-binding proteins, establishing its membership in an NMD complex [#1]. Despite the machinery being expressed and intact, CRISPR-Cas9 disruption of PF3D7_0925800 does not lead to accumulation or degradation of bulk nonsense transcripts and does not impair asexual blood-stage growth, indicating that UPF2-dependent NMD is non-essential for global mRNA quality control and parasite viability under these conditions [#2]. However, loss of NMD pathway function, including UPF2, stabilizes the var2csa transcript in 'switcher' lines, consistent with NMD selectively degrading incompletely translated var2csa mRNA via an upstream ORF in its 5'-UTR to promote activation of an alternative var gene [#3]. Beyond these findings, the biochemical mechanism by which PF3D7_0925800 recognizes or licenses target transcripts has not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"It was unknown where UPF2 acts in the parasite; epitope-tagging placed the protein in cytoplasmic puncta, giving a subcellular context for its function.\",\n      \"evidence\": \"CRISPR-Cas9 epitope-tagging and fluorescence microscopy in P. falciparum\",\n      \"pmids\": [\"37366629\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Nature and composition of the puncta not defined\",\n        \"Whether localization changes across the parasite life cycle not addressed\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether PF3D7_0925800 assembles into a functional NMD complex was unresolved; Co-IP demonstrated physical interaction with PfUPF1 and other mRNA-binding proteins, establishing its membership in an NMD complex.\",\n      \"evidence\": \"Co-immunoprecipitation following CRISPR-Cas9 epitope-tagging in P. falciparum\",\n      \"pmids\": [\"37366629\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single Co-IP without reciprocal validation\",\n        \"Stoichiometry and full composition of the complex not defined\",\n        \"Direct versus bridged interaction with UPF1 not distinguished\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The functional requirement for UPF2-dependent NMD was untested; knockout showed no bulk nonsense-transcript degradation and no growth defect, establishing that this pathway is dispensable for global mRNA quality control and asexual viability.\",\n      \"evidence\": \"CRISPR-Cas9 knockout with RNA-seq of nonsense transcript abundance and growth assay in P. falciparum\",\n      \"pmids\": [\"37366629\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether UPF2 has non-canonical or stage-specific roles not addressed\",\n        \"Whether a subset of transcripts requires UPF2 not resolved by bulk RNA-seq\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"It was unclear whether NMD had any specific substrate given its dispensability for bulk decay; disruption of the pathway stabilized var2csa mRNA, showing NMD selectively degrades this uORF-containing transcript to regulate var gene switching.\",\n      \"evidence\": \"NMD pathway knockout, RNA-seq, var2csa transcript stability measurement and uORF start-codon mutagenesis in P. falciparum switcher lines\",\n      \"pmids\": [\"41851501\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"UPF2 contribution inferred from pathway disruption rather than a UPF2-specific experiment\",\n        \"Direct binding of UPF2 to var2csa mRNA not demonstrated\",\n        \"Generality across other var genes not established\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular mechanism by which PF3D7_0925800 recognizes uORF-containing or incompletely translated transcripts and licenses their decay remains unknown.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct RNA-binding or substrate-recognition experiment for UPF2\",\n        \"No structural model of the parasite NMD complex\",\n        \"Mechanism linking uORF translation to UPF2-dependent decay unresolved\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005737\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0000184\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"complexes\": [\n      \"NMD complex containing PfUPF1 (PF3D7_1005500) and other mRNA-binding proteins\"\n    ],\n    \"partners\": [\n      \"PfUPF1 (PF3D7_1005500)\"\n    ],\n    \"other_free_text\": [\n      \"PF3D7_0925800 disruption does not degrade bulk nonsense transcripts and does not impair asexual blood-stage growth [#2]\",\n      \"NMD pathway disruption stabilizes the uORF-containing var2csa transcript, linking the pathway to var gene switching [#3]\",\n      \"UPF2-specific contribution to var2csa regulation is inferred from pathway disruption rather than a UPF2-specific experiment [#3]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0925800","name":null,"product":"regulator of nonsense transcripts 2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0826600","name":null,"product":"regulator of nonsense transcripts 2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0723700","name":null,"product":"regulator of nonsense transcripts 2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"UPF2","evaluation":null}