{"gene":"RPF2","run_date":"2026-06-10T06:43:37","timeline":{"discoveries":[{"year":2007,"finding":"Rpf2 and Rrs1 form a ribonucleoprotein neighborhood in preribosomes together with ribosomal proteins rpL5, rpL11, and 5S rRNA; Rpf2 and Rrs1 are required for recruiting rpL5, rpL11, and 5S rRNA into 90S preribosomal particles, and in their absence, processing of 27SB pre-rRNA is blocked, causing abortive 66S pre-rRNPs to be prematurely released from the nucleolus to the nucleoplasm without cytoplasmic export.","method":"In vitro binding assays, genetic depletion/co-immunoprecipitation in yeast, subcellular fractionation and localization","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal in vitro binding assays plus genetic depletion with defined pre-rRNA processing phenotype and localization readout, independently foundational study","pmids":["17938242"],"is_preprint":false},{"year":2015,"finding":"Crystal structure of the Rpf2-Rrs1 complex (Aspergillus nidulans) at 1.5 Å reveals that the Brix domain of Rpf2 is completed by Rrs1 to form two anticodon-binding-like domains; the heterodimer makes specific contacts with 5S rRNA, RpL5, and the biogenesis factor Rsa4; flexible C-terminal tails of Rrs1 occupy the central protuberance and block rotation of 25S rRNA and the 5S RNP, explaining why removal of Rpf2-Rrs1 is required for the rearrangements that drive 60S maturation.","method":"X-ray crystallography at 1.5 Å, fitting into cryo-EM density of pre-60S particle, biochemical binding data","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional validation by cryo-EM fitting and biochemical correlation, replicated independently by a concurrent crystal structure study","pmids":["26117542"],"is_preprint":false},{"year":2015,"finding":"Crystal structure of the Aspergillus nidulans Rpf2-Rrs1 core complex shows the N-terminal Brix domain of Rpf2 interlocked with the N-terminal domain of Rrs1 (whose long α-helix joins the C-terminal half of the Brix domain); gel-shift analysis confirmed direct binding of the Rpf2-Rrs1 complex to 5S rRNA, and mutagenesis identified Rpf2 R236 (R238 in A. nidulans) as critical for this binding.","method":"X-ray crystallography, EMSA gel-shift assay, site-directed mutagenesis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with mutagenesis and direct binding assay in a single study","pmids":["25855814"],"is_preprint":false},{"year":2008,"finding":"Human BXDC1 (RPF2) localizes specifically to the nucleolus in HeLa cells and, based on FRAP and RNAi knockdown analyses, functions as a dynamic scaffold protein required for ribosome biogenesis.","method":"Subcellular fractionation, immunofluorescence, FRAP, RNAi knockdown","journal":"Genes to cells : devoted to molecular & cellular mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct nucleolar localization by imaging, FRAP, and RNAi knockdown with ribosome biogenesis phenotype in a single study","pmids":["19170763"],"is_preprint":false},{"year":2017,"finding":"In Trypanosoma brucei, Rpf2 (TbRpf2) was identified as a component of the 5S RNP via tandem affinity purification/mass spectrometry; it mediates conserved binding interactions with 5S rRNA and L5, and additionally interacts with trypanosome-specific proteins P34 and P37; RNAi knockdown of TbRpf2 is lethal and disrupts ribosome formation.","method":"Tandem affinity purification, mass spectrometry, RNAi knockdown with growth and ribosome assembly phenotype","journal":"mSphere","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — TAP-MS identification of complex members plus RNAi functional validation, single lab","pmids":["29062898"],"is_preprint":false},{"year":2023,"finding":"In colorectal cancer cells, RPF2 overexpression upregulates ABCB1 (MDR1) expression and promotes chemotherapy resistance; RPF2 regulates MYCN (an upstream regulator of ABCB1), and CARM1 was found to directly bind MYCN in a manner regulated by RPF2, placing RPF2 in a RPF2→CARM1–MYCN→ABCB1 pathway.","method":"RPF2 overexpression/knockdown in CRC cell lines, Western blot, co-immunoprecipitation of CARM1 and MYCN","journal":"Oncology reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single Co-IP for CARM1-MYCN interaction, mechanistic pathway placement indirect","pmids":["37997821"],"is_preprint":false},{"year":2024,"finding":"RPF2 promotes epithelial-mesenchymal transition (EMT) and metastasis in colorectal cancer cells via activation of the AKT/GSK-3β signaling pathway; CARM1 was identified as a key downstream effector of RPF2, and selective CARM1 inhibition suppressed RPF2-induced AKT/GSK-3β activation and EMT; these findings were confirmed in vitro and in vivo.","method":"Stable RPF2 overexpression/knockdown cell lines, CARM1 inhibitor treatment, in vitro migration/invasion assays, in vivo xenograft experiments, Western blot","journal":"Experimental cell research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, mechanistic pathway placement via pharmacological inhibition without direct biochemical reconstitution of RPF2-CARM1 interaction","pmids":["39674359"],"is_preprint":false}],"current_model":"RPF2 (BXDC1) is a nucleolar ribosome assembly factor that forms a stable heterodimeric complex with Rrs1 via its Brix domain; this complex directly binds 5S rRNA (with R236 critical for binding), ribosomal proteins L5 and L11, and biogenesis factor Rsa4, recruiting the 5S RNP into 90S/pre-60S preribosomal particles and—through C-terminal tails that block 25S rRNA rotation—must itself be removed to allow the structural rearrangements required for 60S subunit maturation; loss of Rpf2 blocks 27SB pre-rRNA processing and causes premature nucleolar release of abortive 66S pre-rRNPs, while in cancer contexts RPF2 has additionally been linked to CARM1-dependent activation of AKT/GSK-3β signaling and chemoresistance, though the mechanistic basis of these latter functions is less well defined."},"narrative":{"mechanistic_narrative":"RPF2 (BXDC1) is a nucleolar ribosome assembly factor that drives incorporation of the 5S ribonucleoprotein into maturing large ribosomal subunits [PMID:17938242, PMID:19170763]. It forms a stable heterodimer with Rrs1 in which the Brix domain of Rpf2 is completed by Rrs1, generating a composite surface that makes specific contacts with 5S rRNA, ribosomal protein L5, and the biogenesis factor Rsa4; binding to 5S rRNA depends on Rpf2 residue R236 [PMID:26117542, PMID:25855814]. Through this complex, Rpf2 and Rrs1 recruit rpL5, rpL11, and 5S rRNA into 90S preribosomal particles, and their loss blocks 27SB pre-rRNA processing and causes abortive 66S pre-rRNPs to be released prematurely from the nucleolus without export [PMID:17938242]. Within the pre-60S particle the flexible Rrs1 C-terminal tails occupy the central protuberance and block rotation of the 25S rRNA and 5S RNP, so removal of the Rpf2-Rrs1 complex is itself required for the rearrangements that complete 60S maturation [PMID:26117542]. The 5S RNP binding role is conserved beyond yeast: in Trypanosoma brucei TbRpf2 binds 5S rRNA and L5 and is essential for ribosome formation [PMID:29062898]. In colorectal cancer cells RPF2 has additionally been linked to CARM1-dependent activation of AKT/GSK-3β signaling, EMT, and ABCB1-mediated chemoresistance [PMID:37997821, PMID:39674359]; the biochemical basis of these signaling functions has not been resolved in the available corpus.","teleology":[{"year":2007,"claim":"Established that Rpf2 and Rrs1 are the factors responsible for delivering the 5S RNP into preribosomes, defining the gene's core role in large-subunit assembly.","evidence":"In vitro binding, genetic depletion/co-IP, and subcellular fractionation in yeast","pmids":["17938242"],"confidence":"High","gaps":["Atomic basis of the 5S rRNA / rpL5 / rpL11 contacts not yet resolved","Mechanism linking 5S RNP recruitment to 27SB processing not defined"]},{"year":2008,"claim":"Extended the assembly-factor role to human cells, showing the orthologous protein BXDC1/RPF2 is a dynamic nucleolar scaffold required for ribosome biogenesis.","evidence":"Immunofluorescence, FRAP, and RNAi knockdown in HeLa cells","pmids":["19170763"],"confidence":"Medium","gaps":["Did not resolve the human-specific binding partners or pre-rRNA processing steps","Scaffold function inferred from dynamics rather than reconstituted biochemistry"]},{"year":2015,"claim":"Resolved the molecular architecture of the Rpf2-Rrs1 heterodimer and explained mechanistically why its removal is a prerequisite for 60S maturation.","evidence":"X-ray crystallography (1.5 Å) with cryo-EM fitting, EMSA, and site-directed mutagenesis (R236)","pmids":["26117542","25855814"],"confidence":"High","gaps":["Does not define the enzymatic machinery that triggers Rpf2-Rrs1 release in vivo","Order of 5S RNP loading relative to other pre-60S events not fully resolved"]},{"year":2017,"claim":"Demonstrated evolutionary conservation of the 5S RNP-binding function while revealing lineage-specific partners, indicating both a conserved core and divergent accessory interactions.","evidence":"TAP-MS and lethal RNAi knockdown in Trypanosoma brucei","pmids":["29062898"],"confidence":"Medium","gaps":["Functional roles of trypanosome-specific partners P34/P37 not defined","Single-lab characterization without structural validation"]},{"year":2024,"claim":"Linked RPF2 to oncogenic signaling, proposing a role in CARM1-dependent AKT/GSK-3β activation, EMT, metastasis, and ABCB1-mediated chemoresistance in colorectal cancer.","evidence":"Overexpression/knockdown cell lines, CARM1 co-IP and pharmacological inhibition, migration/invasion assays, xenografts, Western blot","pmids":["37997821","39674359"],"confidence":"Low","gaps":["No direct biochemical reconstitution of an RPF2-CARM1 interaction; mechanism inferred from pharmacology","Relationship between RPF2's ribosome-assembly role and its signaling phenotype unexplained","Single-lab findings without reciprocal validation"]},{"year":null,"claim":"How RPF2's nucleolar ribosome-assembly function mechanistically connects to its reported cancer signaling roles, and what enzyme catalyzes Rpf2-Rrs1 release in vivo, remain open.","evidence":"","pmids":[],"confidence":"Low","gaps":["No biochemical bridge between 5S RNP assembly and CARM1/AKT signaling","Trigger and timing of Rpf2-Rrs1 dissociation during 60S maturation undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1,2,4]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,3]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[0,3]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,3]}],"complexes":["Rpf2-Rrs1 complex","5S RNP","90S/pre-60S preribosomal particle"],"partners":["RRS1","RPL5","RPL11","RSA4","5S RRNA","P34","P37"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H7B2","full_name":"Ribosome production factor 2 homolog","aliases":["Brix domain-containing protein 1","Ribosome biogenesis protein RPF2 homolog"],"length_aa":306,"mass_kda":35.6,"function":"Involved in ribosomal large subunit assembly. May regulate the localization of the 5S RNP/5S ribonucleoprotein particle to the nucleolus","subcellular_location":"Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/Q9H7B2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPF2","classification":"Common Essential","n_dependent_lines":1181,"n_total_lines":1208,"dependency_fraction":0.9776490066225165},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"FKBP5","stoichiometry":0.2},{"gene":"NPM1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RPF2","total_profiled":1310},"omim":[{"mim_id":"618471","title":"RIBOSOME PRODUCTION FACTOR 2 HOMOLOG; RPF2","url":"https://www.omim.org/entry/618471"},{"mim_id":"614443","title":"EBNA1-BINDING PROTEIN 2; EBNA1BP2","url":"https://www.omim.org/entry/614443"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoli","reliability":"Supported"},{"location":"Nucleoli rim","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Mitotic chromosome","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPF2"},"hgnc":{"alias_symbol":["FLJ21087","bA397G5.4"],"prev_symbol":["BXDC1"]},"alphafold":{"accession":"Q9H7B2","domains":[{"cath_id":"3.40.50.10480","chopping":"28-228","consensus_level":"medium","plddt":94.5881,"start":28,"end":228}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H7B2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H7B2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H7B2-F1-predicted_aligned_error_v6.png","plddt_mean":90.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPF2","jax_strain_url":"https://www.jax.org/strain/search?query=RPF2"},"sequence":{"accession":"Q9H7B2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H7B2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H7B2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H7B2"}},"corpus_meta":[{"pmid":"17938242","id":"PMC_17938242","title":"Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes.","date":"2007","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/17938242","citation_count":167,"is_preprint":false},{"pmid":"15480574","id":"PMC_15480574","title":"The glycosylated cell surface protein Rpf2, containing a resuscitation-promoting factor motif, is involved in intercellular communication of Corynebacterium glutamicum.","date":"2004","source":"Archives of microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/15480574","citation_count":57,"is_preprint":false},{"pmid":"18355281","id":"PMC_18355281","title":"Triple transcriptional control of the resuscitation promoting factor 2 (rpf2) gene of Corynebacterium glutamicum by the regulators of acetate metabolism RamA and RamB and the cAMP-dependent regulator GlxR.","date":"2008","source":"FEMS microbiology letters","url":"https://pubmed.ncbi.nlm.nih.gov/18355281","citation_count":56,"is_preprint":false},{"pmid":"26117542","id":"PMC_26117542","title":"The structure of Rpf2-Rrs1 explains its role in ribosome biogenesis.","date":"2015","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/26117542","citation_count":49,"is_preprint":false},{"pmid":"16734784","id":"PMC_16734784","title":"The Corynebacterium glutamicum gene pmt encoding a glycosyltransferase related to eukaryotic protein-O-mannosyltransferases is essential for glycosylation of the resuscitation promoting factor (Rpf2) and other secreted proteins.","date":"2006","source":"FEMS microbiology letters","url":"https://pubmed.ncbi.nlm.nih.gov/16734784","citation_count":45,"is_preprint":false},{"pmid":"25855814","id":"PMC_25855814","title":"Structural and functional analysis of the Rpf2-Rrs1 complex in ribosome biogenesis.","date":"2015","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/25855814","citation_count":40,"is_preprint":false},{"pmid":"19170763","id":"PMC_19170763","title":"Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleolus.","date":"2008","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/19170763","citation_count":20,"is_preprint":false},{"pmid":"37997821","id":"PMC_37997821","title":"RPF2 mediates the CARM1‑MYCN axis to promote chemotherapy resistance in colorectal cancer cells.","date":"2023","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/37997821","citation_count":7,"is_preprint":false},{"pmid":"29062898","id":"PMC_29062898","title":"Essential Assembly Factor Rpf2 Forms Novel Interactions within the 5S RNP in Trypanosoma brucei.","date":"2017","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/29062898","citation_count":7,"is_preprint":false},{"pmid":"37323230","id":"PMC_37323230","title":"Skim resequencing finely maps the downy mildew resistance loci RPF2 and RPF3 in spinach cultivars whale and Lazio.","date":"2023","source":"Horticulture research","url":"https://pubmed.ncbi.nlm.nih.gov/37323230","citation_count":6,"is_preprint":false},{"pmid":"36499197","id":"PMC_36499197","title":"Fine Mapping and Identification of a Candidate Gene of Downy Mildew Resistance, RPF2, in Spinach (Spinacia oleracea L.).","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36499197","citation_count":4,"is_preprint":false},{"pmid":"39674359","id":"PMC_39674359","title":"RPF2 and CARM1 cooperate to enhance colorectal cancer metastasis via the AKT/GSK-3β signaling pathway.","date":"2024","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/39674359","citation_count":3,"is_preprint":false},{"pmid":"25484219","id":"PMC_25484219","title":"Crystallization and preliminary X-ray crystallographic analysis of ribosome assembly factors: the Rpf2-Rrs1 complex.","date":"2014","source":"Acta crystallographica. Section F, Structural biology communications","url":"https://pubmed.ncbi.nlm.nih.gov/25484219","citation_count":3,"is_preprint":false},{"pmid":"40547146","id":"PMC_40547146","title":"RPF2 regulates the protein kinase B/mammalian target of rapamycin pathway in the pathogenesis of Helicobacter pylori.","date":"2025","source":"World journal of gastrointestinal oncology","url":"https://pubmed.ncbi.nlm.nih.gov/40547146","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8899,"output_tokens":2087,"usd":0.029001,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9010,"output_tokens":2375,"usd":0.052213,"stage2_stop_reason":"end_turn"},"total_usd":0.081214,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"Rpf2 and Rrs1 form a ribonucleoprotein neighborhood in preribosomes together with ribosomal proteins rpL5, rpL11, and 5S rRNA; Rpf2 and Rrs1 are required for recruiting rpL5, rpL11, and 5S rRNA into 90S preribosomal particles, and in their absence, processing of 27SB pre-rRNA is blocked, causing abortive 66S pre-rRNPs to be prematurely released from the nucleolus to the nucleoplasm without cytoplasmic export.\",\n      \"method\": \"In vitro binding assays, genetic depletion/co-immunoprecipitation in yeast, subcellular fractionation and localization\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal in vitro binding assays plus genetic depletion with defined pre-rRNA processing phenotype and localization readout, independently foundational study\",\n      \"pmids\": [\"17938242\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structure of the Rpf2-Rrs1 complex (Aspergillus nidulans) at 1.5 Å reveals that the Brix domain of Rpf2 is completed by Rrs1 to form two anticodon-binding-like domains; the heterodimer makes specific contacts with 5S rRNA, RpL5, and the biogenesis factor Rsa4; flexible C-terminal tails of Rrs1 occupy the central protuberance and block rotation of 25S rRNA and the 5S RNP, explaining why removal of Rpf2-Rrs1 is required for the rearrangements that drive 60S maturation.\",\n      \"method\": \"X-ray crystallography at 1.5 Å, fitting into cryo-EM density of pre-60S particle, biochemical binding data\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional validation by cryo-EM fitting and biochemical correlation, replicated independently by a concurrent crystal structure study\",\n      \"pmids\": [\"26117542\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structure of the Aspergillus nidulans Rpf2-Rrs1 core complex shows the N-terminal Brix domain of Rpf2 interlocked with the N-terminal domain of Rrs1 (whose long α-helix joins the C-terminal half of the Brix domain); gel-shift analysis confirmed direct binding of the Rpf2-Rrs1 complex to 5S rRNA, and mutagenesis identified Rpf2 R236 (R238 in A. nidulans) as critical for this binding.\",\n      \"method\": \"X-ray crystallography, EMSA gel-shift assay, site-directed mutagenesis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with mutagenesis and direct binding assay in a single study\",\n      \"pmids\": [\"25855814\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Human BXDC1 (RPF2) localizes specifically to the nucleolus in HeLa cells and, based on FRAP and RNAi knockdown analyses, functions as a dynamic scaffold protein required for ribosome biogenesis.\",\n      \"method\": \"Subcellular fractionation, immunofluorescence, FRAP, RNAi knockdown\",\n      \"journal\": \"Genes to cells : devoted to molecular & cellular mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct nucleolar localization by imaging, FRAP, and RNAi knockdown with ribosome biogenesis phenotype in a single study\",\n      \"pmids\": [\"19170763\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In Trypanosoma brucei, Rpf2 (TbRpf2) was identified as a component of the 5S RNP via tandem affinity purification/mass spectrometry; it mediates conserved binding interactions with 5S rRNA and L5, and additionally interacts with trypanosome-specific proteins P34 and P37; RNAi knockdown of TbRpf2 is lethal and disrupts ribosome formation.\",\n      \"method\": \"Tandem affinity purification, mass spectrometry, RNAi knockdown with growth and ribosome assembly phenotype\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — TAP-MS identification of complex members plus RNAi functional validation, single lab\",\n      \"pmids\": [\"29062898\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In colorectal cancer cells, RPF2 overexpression upregulates ABCB1 (MDR1) expression and promotes chemotherapy resistance; RPF2 regulates MYCN (an upstream regulator of ABCB1), and CARM1 was found to directly bind MYCN in a manner regulated by RPF2, placing RPF2 in a RPF2→CARM1–MYCN→ABCB1 pathway.\",\n      \"method\": \"RPF2 overexpression/knockdown in CRC cell lines, Western blot, co-immunoprecipitation of CARM1 and MYCN\",\n      \"journal\": \"Oncology reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single Co-IP for CARM1-MYCN interaction, mechanistic pathway placement indirect\",\n      \"pmids\": [\"37997821\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RPF2 promotes epithelial-mesenchymal transition (EMT) and metastasis in colorectal cancer cells via activation of the AKT/GSK-3β signaling pathway; CARM1 was identified as a key downstream effector of RPF2, and selective CARM1 inhibition suppressed RPF2-induced AKT/GSK-3β activation and EMT; these findings were confirmed in vitro and in vivo.\",\n      \"method\": \"Stable RPF2 overexpression/knockdown cell lines, CARM1 inhibitor treatment, in vitro migration/invasion assays, in vivo xenograft experiments, Western blot\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, mechanistic pathway placement via pharmacological inhibition without direct biochemical reconstitution of RPF2-CARM1 interaction\",\n      \"pmids\": [\"39674359\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RPF2 (BXDC1) is a nucleolar ribosome assembly factor that forms a stable heterodimeric complex with Rrs1 via its Brix domain; this complex directly binds 5S rRNA (with R236 critical for binding), ribosomal proteins L5 and L11, and biogenesis factor Rsa4, recruiting the 5S RNP into 90S/pre-60S preribosomal particles and—through C-terminal tails that block 25S rRNA rotation—must itself be removed to allow the structural rearrangements required for 60S subunit maturation; loss of Rpf2 blocks 27SB pre-rRNA processing and causes premature nucleolar release of abortive 66S pre-rRNPs, while in cancer contexts RPF2 has additionally been linked to CARM1-dependent activation of AKT/GSK-3β signaling and chemoresistance, though the mechanistic basis of these latter functions is less well defined.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPF2 (BXDC1) is a nucleolar ribosome assembly factor that drives incorporation of the 5S ribonucleoprotein into maturing large ribosomal subunits [#0, #3]. It forms a stable heterodimer with Rrs1 in which the Brix domain of Rpf2 is completed by Rrs1, generating a composite surface that makes specific contacts with 5S rRNA, ribosomal protein L5, and the biogenesis factor Rsa4; binding to 5S rRNA depends on Rpf2 residue R236 [#1, #2]. Through this complex, Rpf2 and Rrs1 recruit rpL5, rpL11, and 5S rRNA into 90S preribosomal particles, and their loss blocks 27SB pre-rRNA processing and causes abortive 66S pre-rRNPs to be released prematurely from the nucleolus without export [#0]. Within the pre-60S particle the flexible Rrs1 C-terminal tails occupy the central protuberance and block rotation of the 25S rRNA and 5S RNP, so removal of the Rpf2-Rrs1 complex is itself required for the rearrangements that complete 60S maturation [#1]. The 5S RNP binding role is conserved beyond yeast: in Trypanosoma brucei TbRpf2 binds 5S rRNA and L5 and is essential for ribosome formation [#4]. In colorectal cancer cells RPF2 has additionally been linked to CARM1-dependent activation of AKT/GSK-3\\u03b2 signaling, EMT, and ABCB1-mediated chemoresistance [#5, #6]; the biochemical basis of these signaling functions has not been resolved in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established that Rpf2 and Rrs1 are the factors responsible for delivering the 5S RNP into preribosomes, defining the gene's core role in large-subunit assembly.\",\n      \"evidence\": \"In vitro binding, genetic depletion/co-IP, and subcellular fractionation in yeast\",\n      \"pmids\": [\"17938242\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Atomic basis of the 5S rRNA / rpL5 / rpL11 contacts not yet resolved\",\n        \"Mechanism linking 5S RNP recruitment to 27SB processing not defined\"\n      ]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Extended the assembly-factor role to human cells, showing the orthologous protein BXDC1/RPF2 is a dynamic nucleolar scaffold required for ribosome biogenesis.\",\n      \"evidence\": \"Immunofluorescence, FRAP, and RNAi knockdown in HeLa cells\",\n      \"pmids\": [\"19170763\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Did not resolve the human-specific binding partners or pre-rRNA processing steps\",\n        \"Scaffold function inferred from dynamics rather than reconstituted biochemistry\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Resolved the molecular architecture of the Rpf2-Rrs1 heterodimer and explained mechanistically why its removal is a prerequisite for 60S maturation.\",\n      \"evidence\": \"X-ray crystallography (1.5 \\u00c5) with cryo-EM fitting, EMSA, and site-directed mutagenesis (R236)\",\n      \"pmids\": [\"26117542\", \"25855814\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Does not define the enzymatic machinery that triggers Rpf2-Rrs1 release in vivo\",\n        \"Order of 5S RNP loading relative to other pre-60S events not fully resolved\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrated evolutionary conservation of the 5S RNP-binding function while revealing lineage-specific partners, indicating both a conserved core and divergent accessory interactions.\",\n      \"evidence\": \"TAP-MS and lethal RNAi knockdown in Trypanosoma brucei\",\n      \"pmids\": [\"29062898\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional roles of trypanosome-specific partners P34/P37 not defined\",\n        \"Single-lab characterization without structural validation\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked RPF2 to oncogenic signaling, proposing a role in CARM1-dependent AKT/GSK-3\\u03b2 activation, EMT, metastasis, and ABCB1-mediated chemoresistance in colorectal cancer.\",\n      \"evidence\": \"Overexpression/knockdown cell lines, CARM1 co-IP and pharmacological inhibition, migration/invasion assays, xenografts, Western blot\",\n      \"pmids\": [\"37997821\", \"39674359\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct biochemical reconstitution of an RPF2-CARM1 interaction; mechanism inferred from pharmacology\",\n        \"Relationship between RPF2's ribosome-assembly role and its signaling phenotype unexplained\",\n        \"Single-lab findings without reciprocal validation\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RPF2's nucleolar ribosome-assembly function mechanistically connects to its reported cancer signaling roles, and what enzyme catalyzes Rpf2-Rrs1 release in vivo, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No biochemical bridge between 5S RNP assembly and CARM1/AKT signaling\",\n        \"Trigger and timing of Rpf2-Rrs1 dissociation during 60S maturation undefined\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 2, 4]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"complexes\": [\n      \"Rpf2-Rrs1 complex\",\n      \"5S RNP\",\n      \"90S/pre-60S preribosomal particle\"\n    ],\n    \"partners\": [\n      \"RRS1\",\n      \"RPL5\",\n      \"RPL11\",\n      \"RSA4\",\n      \"5S rRNA\",\n      \"P34\",\n      \"P37\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}