Affinage

RPF2

Ribosome production factor 2 homolog · UniProt Q9H7B2

Length
306 aa
Mass
35.6 kDa
Annotated
2026-06-10
14 papers in source corpus 7 papers cited in narrative 7 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

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.

Mechanistic history

Synthesis pass · year-by-year structured walk · 5 steps
  1. 2007 High

    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

    PMID:17938242

    Open questions at the time
    • Atomic basis of the 5S rRNA / rpL5 / rpL11 contacts not yet resolved
    • Mechanism linking 5S RNP recruitment to 27SB processing not defined
  2. 2008 Medium

    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

    PMID:19170763

    Open questions at the time
    • Did not resolve the human-specific binding partners or pre-rRNA processing steps
    • Scaffold function inferred from dynamics rather than reconstituted biochemistry
  3. 2015 High

    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)

    PMID:25855814 PMID:26117542

    Open questions at the time
    • 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
  4. 2017 Medium

    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

    PMID:29062898

    Open questions at the time
    • Functional roles of trypanosome-specific partners P34/P37 not defined
    • Single-lab characterization without structural validation
  5. 2024 Low

    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

    PMID:37997821 PMID:39674359

    Open questions at the time
    • 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

Open questions

Synthesis pass · forward-looking unresolved questions
  • 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.
  • No biochemical bridge between 5S RNP assembly and CARM1/AKT signaling
  • Trigger and timing of Rpf2-Rrs1 dissociation during 60S maturation undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 4 GO:0005198 structural molecule activity 2
Localization
GO:0005730 nucleolus 2
Pathway
R-HSA-8953854 Metabolism of RNA 2
Complex memberships
5S RNP90S/pre-60S preribosomal particleRpf2-Rrs1 complex

Evidence

Reading pass · 7 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 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. In vitro binding assays, genetic depletion/co-immunoprecipitation in yeast, subcellular fractionation and localization Genes & development High 17938242
2015 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. X-ray crystallography at 1.5 Å, fitting into cryo-EM density of pre-60S particle, biochemical binding data Nucleic acids research High 26117542
2015 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. X-ray crystallography, EMSA gel-shift assay, site-directed mutagenesis Nucleic acids research High 25855814
2008 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. Subcellular fractionation, immunofluorescence, FRAP, RNAi knockdown Genes to cells : devoted to molecular & cellular mechanisms Medium 19170763
2017 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. Tandem affinity purification, mass spectrometry, RNAi knockdown with growth and ribosome assembly phenotype mSphere Medium 29062898
2023 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. RPF2 overexpression/knockdown in CRC cell lines, Western blot, co-immunoprecipitation of CARM1 and MYCN Oncology reports Low 37997821
2024 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. Stable RPF2 overexpression/knockdown cell lines, CARM1 inhibitor treatment, in vitro migration/invasion assays, in vivo xenograft experiments, Western blot Experimental cell research Low 39674359

Source papers

Stage 0 corpus · 14 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2007 Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. Genes & development 167 17938242
2004 The glycosylated cell surface protein Rpf2, containing a resuscitation-promoting factor motif, is involved in intercellular communication of Corynebacterium glutamicum. Archives of microbiology 57 15480574
2008 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. FEMS microbiology letters 56 18355281
2015 The structure of Rpf2-Rrs1 explains its role in ribosome biogenesis. Nucleic acids research 49 26117542
2006 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. FEMS microbiology letters 45 16734784
2015 Structural and functional analysis of the Rpf2-Rrs1 complex in ribosome biogenesis. Nucleic acids research 40 25855814
2008 Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleolus. Genes to cells : devoted to molecular & cellular mechanisms 20 19170763
2023 RPF2 mediates the CARM1‑MYCN axis to promote chemotherapy resistance in colorectal cancer cells. Oncology reports 7 37997821
2017 Essential Assembly Factor Rpf2 Forms Novel Interactions within the 5S RNP in Trypanosoma brucei. mSphere 7 29062898
2023 Skim resequencing finely maps the downy mildew resistance loci RPF2 and RPF3 in spinach cultivars whale and Lazio. Horticulture research 6 37323230
2022 Fine Mapping and Identification of a Candidate Gene of Downy Mildew Resistance, RPF2, in Spinach (Spinacia oleracea L.). International journal of molecular sciences 4 36499197
2024 RPF2 and CARM1 cooperate to enhance colorectal cancer metastasis via the AKT/GSK-3β signaling pathway. Experimental cell research 3 39674359
2014 Crystallization and preliminary X-ray crystallographic analysis of ribosome assembly factors: the Rpf2-Rrs1 complex. Acta crystallographica. Section F, Structural biology communications 3 25484219
2025 RPF2 regulates the protein kinase B/mammalian target of rapamycin pathway in the pathogenesis of Helicobacter pylori. World journal of gastrointestinal oncology 0 40547146

Missed literature

Know a paper Affinage missed for RPF2? Flag it for the maintainers and the community.

No submissions yet.