RPF1

The RPF1 symbol maps to two unrelated proteins in this corpus, and the timeline coheres into two internally consistent mechanistic pictures. In ribosome biogenesis, yeast and human RPF1 is a nucleolar pre-60S assembly factor: yeast Rpf1 belongs to the Imp4 superfamily defined by a sigma(70)-like RNA-binding domain and is required for a specific stage of large-subunit biogenesis (PMID:11864606). It is delivered to the nucleus by the import receptor Kap120 (with parallel routes via Kap114 and Nmd5), as Kap120 binds Rpf1 directly and is released by Ran-GTP, and loss of either factor traps 60S particles in the nucleus (PMID:16581791). Within early nucleolar pre-60S intermediates, Rpf1 is an integral member of the Nsa1-Rrp1-Rpf1-Mak16 module that stabilizes the solvent-exposed face of the maturing 60S subunit (PMID:29245012), a function that depends on the [4Fe-4S] cluster of its partner Mak16, whose oxidative disruption breaks the Mak16-Rpf1 interaction and lowers 25S rRNA levels, placing Rpf1 at a redox-sensitive step of 60S maturation (PMID:41231949). Human RPF1 is the conserved counterpart, associating with pre-60S (not pre-40S) particles and acting within a WDR74-RPF1-MAK16-RRP1 module whose members are mutually required for their interaction with the helicase MTR4 and for accurate pre-rRNA cleavage; RPF1 itself does not catalyze cleavage but promotes the pre-rRNA conformation that favors it (PMID:38391939, PMID:39706051). Distinctly, the POU6F2/RPF-1 entries describe a POU-domain transcription factor: it binds octamer/POU consensus DNA in an isoform-dependent manner requiring an N-terminal Ser-rich region (PMID:8601806, PMID:27425396), transactivates developmental promoters including Prop1 and Prrx2 in pituitary progenitors (PMID:24804940), and on induction localizes to the nucleus, suppresses proliferation, and reduces tumor xenograft growth (PMID:27425396).

1. 2002 Medium

   Established that yeast Rpf1 is an RNA-binding protein of the Imp4/sigma(70)-like superfamily functionally required for a defined stage of ribosome biogenesis, defining its molecular class.

   Evidence Bioinformatic domain identification plus genetic requirement analysis in yeast

   PMID:11864606

   Open questions at the time

   • Did not define which biogenesis substep or partner particle
   • RNA target of the sigma(70)-like domain not directly mapped
2. 2006 High

   Answered how Rpf1 reaches the nucleolus, showing Kap120 is a direct import receptor (with parallel Kap114/Nmd5 routes) and that the nuclear 60S accumulation defect reflects failed Rpf1 import rather than a direct export role.

   Evidence Two-hybrid, in vitro binding, Ran-GTP release, and genetic epistasis/overexpression suppression in yeast

   PMID:16581791

   Open questions at the time

   • Import signal on Rpf1 not delimited
   • Relative contribution of the three parallel importins unquantified
3. 2013 Medium

   Placed Rpf1 in a functional network with Mak5, Rpl14, Ebp2 and Nop16 implicated in shaping a eukaryote-specific 60S surface, linking it physically/genetically to the Nsa1 pre-60S particle.

   Evidence Synthetic lethal genetic screens and co-IP of Mak5 with the Nsa1 particle

   PMID:24312670

   Open questions at the time

   • Direct Rpf1 contacts within the particle not resolved
   • Genetic interactions do not prove direct binding
4. 2017 High

   Resolved Rpf1's structural position by mapping it within the Nsa1-Rrp1-Rpf1-Mak16 module that stabilizes the solvent face of the 60S subunit across sequential early nucleolar intermediates.

   Evidence Cryo-EM of six pre-60S assembly states at 3.3-4.5 Å with assembly-factor mapping

   PMID:29245012

   Open questions at the time

   • Functional consequence of each contact not tested by mutagenesis
   • Order of module release during maturation not fully defined
5. 2024 Medium

   Extended the role to human RPF1, showing it associates specifically with pre-60S particles and shapes pre-rRNA conformation to enable correct cleavage of 47S-derived precursors rather than catalyzing cleavage itself.

   Evidence siRNA/shRNA knockdown in HEK293, pre-rRNA processing analysis, particle association assays

   PMID:38391939

   Open questions at the time

   • Direct RNA-binding by human RPF1 not demonstrated
   • Single cell line, single lab
6. 2024 Medium

   Defined the human module as WDR74-RPF1-MAK16-RRP1 whose members are mutually required for engaging the helicase MTR4 and for accurate pre-rRNA cleavage, establishing interdependence within the module.

   Evidence Co-IP/mass spectrometry and functional knockdown

   PMID:39706051

   Open questions at the time

   • Direct vs. indirect RPF1-MTR4 contact not distinguished
   • Stoichiometry and assembly order of the module unresolved
7. 2025 High

   Identified a redox control point in early 60S maturation by showing the Mak16 [4Fe-4S] cluster is required for the Mak16-Rpf1 interaction, with oxidative stress disrupting the complex and lowering 25S rRNA.

   Evidence In vitro/in vivo Fe/S characterization, co-IP under H2O2, and rRNA quantification after cluster-disrupting mutagenesis in yeast

   PMID:41231949

   Open questions at the time

   • Whether Rpf1 itself senses redox is not addressed
   • Physiological oxidative conditions that engage this switch not defined
8. 1996 Medium

   Characterized the unrelated POU6F2/RPF-1 as a POU-domain transcription factor with isoform-dependent octamer DNA binding, expressed during retinal ganglion/amacrine cell development.

   Evidence In vitro DNA-binding assay with isoform comparison, cloning, and in situ hybridization in mouse retina

   PMID:8601806

   Open questions at the time

   • In vivo target genes in retina not identified
   • Functional consequence of the splice insert on transcription not tested
9. 2014 Medium

   Showed POU6F2/RPF-1 binds pituitary gene regulatory regions and transactivates Prop1 and Prrx2 (but not Prrx1) in progenitor cells, implicating it in pituitary developmental gene regulation.

   Evidence Yeast one-hybrid, luciferase reporter assays, in situ hybridization and RT-PCR in rat pituitary

   PMID:24804940

   Open questions at the time

   • Direct in vivo promoter occupancy not confirmed by ChIP
   • Endogenous requirement for Prop1/Prrx2 regulation not tested by loss-of-function
10. 2016 High

    Established human POU6F2/RPF-1 as a nuclear, sequence-specific transcriptional activator whose Ser-rich N-terminal region is required for DNA binding and whose induction suppresses proliferation and tumor growth, defining genome-wide candidate targets.

    Evidence Inducible transfection, EMSA with competition and deletion mutagenesis, reporter assays, ChIP-chip, transcriptome profiling, and xenograft assays

    PMID:27425396

    Open questions at the time

    • Mechanism linking transcriptional targets to growth suppression not resolved
    • Direct vs. indirect status of the 217 candidate targets not validated individually

• It remains unresolved whether the sigma(70)-like RNA-binding activity of the ribosome-biogenesis RPF1 engages a specific pre-rRNA element, and the corpus does not reconcile the two distinct proteins sharing the RPF1 symbol.
• Direct RNA target of the sigma(70)-like domain unidentified
• No structural/functional data on human RPF1 contacts within the 60S particle