KRR1

KRR1 (Krr1p) is a conserved, essential nucleolar protein that functions in early biogenesis of the small (40S) ribosomal subunit as a component of the small-subunit (SSU) processome/90S pre-ribosome (PMID:11027267, PMID:15590835). It is specifically required for production of 18S rRNA: its depletion blocks pre-rRNA processing and reduces 18S and 20S pre-rRNA levels without affecting 25S rRNA, placing it genetically upstream of the rpS14-18S rRNA assembly interaction (PMID:11027267). Krr1 is built from two packed KH domains with divergent roles: KH1, which lacks the canonical RNA-binding GXXG motif, binds the assembly factor Kri1, while the canonical KH2 surface engages an α-helix of the assembly factor Faf1 (PMID:11027267, PMID:15178413, PMID:24990943). The Krr1-Faf1 interaction does not control incorporation of either protein into pre-ribosomes but maintains a critical 90S conformation needed for early cleavage at sites A0, A1, and A2, and its disruption is lethal (PMID:24990943). Within the assembling particle, the snR30 snoRNP coordinates recruitment of a Krr1-Utp23-Kri1 subcomplex and ribosomal proteins uS11-uS15, and Krr1-dependent release of snR30 drives integration of the platform subdomain into the 90S pre-ribosome (PMID:40399280). This biogenesis role is conserved in mammals, where Krr1 supports 18S rRNA production, global translation, and maintenance of pluripotency factor levels in mouse embryonic stem cells (PMID:26443847).

1. 2000 High

   Established that Krr1p is a nucleolar factor dedicated to small-subunit biogenesis rather than general ribosome production, defining its pathway specificity.

   Evidence Nucleolar localization, polysome analysis, pulse-chase and Northern blot in temperature-sensitive and shutoff yeast strains

   PMID:11027267

   Open questions at the time

   • Did not identify which pre-rRNA cleavage step is directly catalyzed or chaperoned
   • No structural basis for substrate specificity
2. 2000 High

   Identified Kri1p as a direct physical partner and linked the interaction functionally to 40S biogenesis, providing the first protein-interaction anchor for Krr1.

   Evidence Reciprocal co-immunoprecipitation, two-hybrid, and temperature-sensitive mutant defective in Kri1p binding in yeast

   PMID:11027267

   Open questions at the time

   • Interaction surface on Krr1 not mapped at this stage
   • Order of recruitment relative to other factors unknown
3. 2000 Medium

   Placed Krr1p upstream of the rpS14-18S rRNA interaction in 40S assembly through genetic epistasis.

   Evidence Multicopy suppression of krr1-ts by RPS14A and loss of suppression by an rpS14 truncation with reduced 18S binding

   PMID:11027267

   Open questions at the time

   • Genetic suppression does not establish direct physical contact with rpS14
   • Mechanism by which Krr1 promotes rpS14 loading unresolved
4. 2000 Medium

   Confirmed essentiality and growth-phase-restricted expression, tying Krr1p function to active cell division.

   Evidence Gene deletion, fractionation/immunofluorescence localization, and growth-phase expression analysis in yeast

   PMID:11996121

   Open questions at the time

   • Regulation of growth-phase expression not mechanistically defined
5. 2004 Medium

   Defined Krr1p as a bona fide SSU processome subunit, integrating it into a defined large RNP complex.

   Evidence Co-immunoprecipitation with Mpp10, U3 snoRNA, and pre-rRNAs in yeast

   PMID:15590835

   Open questions at the time

   • Did not establish direct vs indirect association with U3 snoRNA
   • Position within the processome architecture unknown
6. 2004 Medium

   Identified Faf1p as a second direct Krr1 partner whose depletion phenocopies Krr1 loss at A0/A1/A2 processing, expanding the interaction network controlling 18S production.

   Evidence Two-hybrid with Krr1p bait plus depletion and Northern blot rRNA-processing analysis in yeast

   PMID:15178413

   Open questions at the time

   • Whether Faf1 binding is required for the same step as Kri1 binding unresolved at this stage
   • No structural detail of the interface
7. 2004 Medium

   Broadened the physical interaction landscape of Krr1 to multiple ribosomal proteins and linked genetic suppressors to translation and rRNA modification factors.

   Evidence Tandem affinity purification and multicopy suppressor screen of the cold-sensitive krr1-21 mutant in yeast

   PMID:15094838

   Open questions at the time

   • TAP interactions may reflect complex co-purification rather than direct contacts
   • Functional relevance of individual suppressors not dissected
8. 2014 High

   Resolved the dual-KH architecture of Krr1 and assigned distinct partner-binding roles to KH1 (Kri1) and KH2 (Faf1), explaining how one protein bridges two assembly factors.

   Evidence 2.8 Å co-crystal structure of the Krr1 core with a Faf1 fragment, interface mutagenesis, and in vivo assays

   PMID:24990943

   Open questions at the time

   • Structure of the KH1-Kri1 interface not directly solved
   • RNA-binding role of the canonical KH2 surface not separated from Faf1 binding
9. 2014 High

   Showed the Krr1-Faf1 contact maintains a required 90S conformation for early processing rather than controlling factor incorporation, refining the mechanistic role from recruitment to conformational scaffolding.

   Evidence Structure-guided interface mutagenesis with rRNA-processing, viability, and pre-ribosome incorporation readouts in yeast

   PMID:24990943

   Open questions at the time

   • The precise conformational change stabilized is not visualized
   • How conformation couples to A0/A1/A2 cleavage chemistry is unknown
10. 2015 Medium

    Extended Krr1 function to mammals and connected ribosome biogenesis to pluripotency, demonstrating physiological consequences beyond yeast.

    Evidence RNAi knockdown in mouse ESCs with 18S biogenesis, translation rate, and pluripotency factor readouts

    PMID:26443847

    Open questions at the time

    • Direct molecular interactions of mammalian KRR1 not mapped
    • Whether pluripotency effect is purely translational is not fully resolved
11. 2025 High

    Placed Krr1 in a defined assembly sequence in which snR30 coordinates recruitment of a Krr1-Utp23-Kri1 subcomplex and uS11-uS15, with Krr1-dependent snR30 release enabling platform integration into the 90S.

    Evidence Cryo-EM of 90S pre-ribosomes with RNA hybridization blocking and biochemical reconstitution

    PMID:40399280

    Open questions at the time

    • The molecular trigger for Krr1-dependent snR30 release is not defined
    • Whether Krr1 acts catalytically or sterically in release is unresolved

• How Krr1-stabilized 90S conformation and snR30 release are mechanistically coupled to the chemistry of A0/A1/A2 cleavage remains unresolved.
• No structure capturing the cleavage-competent state
• The catalytic nuclease(s) acted upon by Krr1-dependent conformational changes not connected to Krr1 directly