Affinage

RRP9

U3 small nucleolar RNA-interacting protein 2 · UniProt O43818

Length
475 aa
Mass
51.8 kDa
Annotated
2026-06-10
17 papers in source corpus 13 papers cited in narrative 13 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

RRP9 (U3-55K) is a WD-repeat core component of the U3 snoRNP that organizes early steps of small-subunit ribosome biogenesis by binding U3 snoRNA and promoting pre-rRNA cleavage required for 18S rRNA maturation (PMID:10982864, PMID:31996908). Its WD-repeat domain folds into a seven-bladed beta-propeller whose conserved '7bc loop' surface specifically recognizes the Box B/C motif unique to U3 snoRNA; this recognition, together with C-terminal sequences, drives both U3 association and nucleolar localization, and is enhanced by prior loading of Snu13 on the B/C motif (PMID:10982864, PMID:23509373). A surface opposite the RNA-binding face mediates a direct protein-protein contact with Rrp36 and cooperates with U3/pre-rRNA base-pairing to stabilize the SSU processome and support cleavage at sites A1 and A2 (PMID:31996908). RRP9 function in pre-rRNA processing is regulated by post-translational modification: SIRT7-mediated deacetylation enhances U3 snoRNA binding and is reversed under stress by nucleolar release of SIRT7 (PMID:26867678), and Smurf1-catalyzed neddylation at Lys221 (reversed by NEDP1) is required for productive processing, with the K221R mutant failing to support pre-rRNA processing or tumor cell proliferation (PMID:34662580). Beyond its nucleolar role, RRP9 has been linked to oncogenic AKT signaling through physical interactions with IGF2BP1 (PMID:36434608), SQSTM1 (PMID:40994061), and JUN (PMID:39702367), and its expression is controlled transcriptionally by MYC and post-transcriptionally by METTL1-mediated m7G mRNA modification (PMID:40781078, PMID:39960239).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2000 High

    Established how RRP9 is recruited to its specific RNA target, answering whether U3-55K associates with U3 snoRNA directly and which RNA elements confer specificity.

    Evidence In vivo and in vitro RNA binding with Box B/C mutagenesis and WD-repeat deletion analysis in Xenopus U3-55k

    PMID:10982864

    Open questions at the time
    • Atomic basis of the WD/U3 contact not resolved
    • Contribution of protein partners to recruitment not quantified
  2. 2013 High

    Defined the structural basis of U3 recognition, showing the WD domain forms a beta-propeller and identifying the specific surface loop responsible for RNA binding and nucleolar targeting.

    Evidence X-ray crystallography of yeast and human WD domains with surface-patch mutagenesis and yeast growth assays

    PMID:23509373

    Open questions at the time
    • No structure of the full RRP9/U3/Snu13 assembly
    • Role of N-terminal NLS in context of intact processome unresolved
  3. 2016 High

    Showed RRP9's RNA-binding activity is acetylation-regulated, linking pre-rRNA processing to stress signaling via SIRT7.

    Evidence Reciprocal Co-IP, SIRT7 knockdown, deacetylation and RNA-binding assays with stress-response validation

    PMID:26867678

    Open questions at the time
    • Specific acetylated lysines not mapped
    • Acetyltransferase responsible not identified
  4. 2020 High

    Identified a second functional surface on the propeller that contacts Rrp36 and cooperates with U3/pre-rRNA base-pairing, explaining how RRP9 stabilizes the SSU processome for A1/A2 cleavage.

    Evidence R289A site-directed mutagenesis, pre-rRNA processing assays, interaction mapping, and genetic epistasis with U3 variants in yeast

    PMID:31996908

    Open questions at the time
    • Structural detail of the Rrp36 contact unknown
    • Human ortholog interaction with RRP36 not directly tested
  5. 2021 High

    Revealed a neddylation switch (Smurf1/NEDP1 at Lys221) controlling RRP9 processing activity and tying it to tumor cell proliferation.

    Evidence In vitro/in vivo neddylation reconstitution, Co-IP, K221R mutagenesis, and processing/proliferation rescue assays

    PMID:34662580

    Open questions at the time
    • How neddylation alters RRP9 conformation or partner binding unresolved
    • Interplay between neddylation and acetylation not addressed
  6. 2022 Medium

    Began defining a non-canonical role, showing RRP9 binds IGF2BP1 to activate AKT signaling and confer chemoresistance in pancreatic cancer.

    Evidence Co-IP, co-localization, KD/OE with apoptosis and xenograft assays plus AKT-inhibitor rescue

    PMID:36434608

    Open questions at the time
    • Whether this role is independent of ribosome biogenesis unclear
    • Direct mechanism linking IGF2BP1 binding to AKT not defined
  7. 2024 Medium

    Extended the oncogenic interaction network, showing RRP9 stabilizes JUN by limiting MDM2-mediated ubiquitination.

    Evidence Co-IP, ubiquitination and protein stability assays, shRNA knockdown with rescue in breast cancer cells

    PMID:39702367

    Open questions at the time
    • Single lab without reciprocal validation across systems
    • Direct vs indirect effect of RRP9 on MDM2 not separated
  8. 2025 Medium

    Mapped upstream regulation of RRP9 expression, identifying MYC transcriptional control and METTL1 m7G-dependent mRNA stabilization, and tied RRP9 to nucleolar size and rRNA synthesis in cancer cells.

    Evidence Transcriptomics, MeRIP and actinomycin D mRNA stability assays, KD/OE with rRNA synthesis and nucleolar measurements in AML cells

    PMID:39960239 PMID:40781078

    Open questions at the time
    • Direct MYC binding to RRP9 promoter not shown
    • m7G reader linking modification to translation/stability not identified
  9. 2025 Low

    Reported additional cancer-context partners (SQSTM1) and downstream signaling outputs (AKT/GSK3β/β-catenin, E2F1/CDK1), broadening the proposed oncogenic functions.

    Evidence FLAG pull-down/MS with Co-IP for SQSTM1; western blot pathway placement and reporter/functional assays for AKT and E2F1-CDK1 axes

    PMID:40526312 PMID:40937881 PMID:40994061

    Open questions at the time
    • AKT and E2F1 axes placed by western blot/rescue without direct RRP9 binding to pathway components
    • Single-lab observations not independently confirmed
  10. 2026 Low

    Reported a context-dependent tumor-suppressive role in hepatocellular carcinoma via PI3K/AKT/mTOR inhibition and CCNA2 downregulation, contrasting the oncogenic AKT activation seen in other cancers.

    Evidence Lentiviral KD/OE, transcriptomics, western blot, PI3K modulator rescue, and xenograft in mice

    PMID:41952494

    Open questions at the time
    • RRP9-CCNA2 association not validated by direct binding assay
    • Reconciliation of opposing AKT effects across tissues unresolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • How RRP9's conserved nucleolar pre-rRNA processing function mechanistically connects to its reported cytoplasmic/oncogenic AKT-modulating interactions, and why effects on AKT signaling differ across cancer types, remains unresolved.
  • No structural or biochemical link between ribosome-biogenesis role and signaling partners
  • Opposing oncogenic vs tumor-suppressive outcomes not mechanistically reconciled

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 3
Localization
GO:0005730 nucleolus 4
Pathway
R-HSA-1852241 Organelle biogenesis and maintenance 3 R-HSA-8953854 Metabolism of RNA 3
Partners
IGF2BP1JUNRRP36SIRT7SMURF1SNU13SQSTM1
Complex memberships
SSU processomeU3 snoRNP

Evidence

Reading pass · 13 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2000 U3-55k (RRP9) interaction with U3 snoRNA in vivo is mediated by the Box B/C motif unique to U3 snoRNA; mutation of Box B and Box C disrupted the interaction, while Box C appears to be the primary determinant in vitro. WD repeats and C-terminal sequences of U3-55k are required for U3 RNA association and nucleolar localization, suggesting protein-protein interactions also contribute. In vivo RNA binding assays (mutation of U3 Box B/C), in vitro RNA binding assays, cDNA cloning of Xenopus U3-55k, deletion mutagenesis of WD repeats Nucleic Acids Research High 10982864
2013 Crystal structures of the WD repeat domain of yeast Rrp9 and its human ortholog U3-55K were determined, revealing a seven-bladed beta-propeller fold. A conserved '7bc loop' on the WD domain surface is crucial for specific recognition of U3 snoRNA, nucleolar localization of Rrp9, and yeast growth. Prior association of Snu13 with the B/C motif enhances specific binding of the WD domain. The N-terminal region contains a bipartite nuclear localization signal that is dispensable for nucleolar localization. X-ray crystallography, mutagenesis of conserved surface patches, yeast growth assays, biochemical binding assays RNA High 23509373
2016 SIRT7 deacetylates U3-55k (RRP9), a core component of the U3 snoRNP complex. Deacetylation of U3-55k by SIRT7 enhances U3-55k binding to U3 snoRNA, which is required for pre-rRNA processing (early cleavage steps for 18S rRNA generation). Under stress, SIRT7 is released from nucleoli, causing hyperacetylation of U3-55k and attenuation of pre-rRNA processing. Co-immunoprecipitation (SIRT7–U3-55k interaction), knockdown of SIRT7, acetylation/deacetylation assays, RNA binding assays, nucleolar localization experiments Nature Communications High 26867678
2020 The R289A substitution in the Rrp9 beta-propeller domain (surface opposite to U3 snoRNA binding face) specifically reduced pre-rRNA cleavage at sites A1 and A2. A direct protein-protein interaction between the Rrp9 beta-propeller domain and Rrp36 was identified; the R289A mutation reduced this interaction, implicating it in the processing phenotype. Synergistic negative interactions were observed between R289A and U3 mutations that destabilize U3/pre-rRNA base-pairing, indicating cooperative function in SSU-processome stability. Site-directed mutagenesis (R289A), pre-rRNA processing assays, protein-protein interaction network mapping, genetic epistasis/synergy analysis with U3 variants Nucleic Acids Research High 31996908
2021 RRP9 is neddylated at Lys221 by the HECT-type E3 ligase Smurf1; this neddylation is removed by the NEDP1 deneddylase. RRP9 neddylation is required for pre-rRNA processing and ribosomal biogenesis; the unneddylated K221R mutant fails to promote pre-rRNA processing and does not support tumor cell proliferation, colony formation, or migration. In vivo and in vitro neddylation assays, Co-immunoprecipitation (Smurf1–RRP9), site-directed mutagenesis (K221R), pre-rRNA processing assays, functional cell proliferation/migration assays Journal of Biological Chemistry High 34662580
2022 RRP9 interacts with the DNA-binding region of IGF2BP1 in pancreatic cancer cells, activating the AKT signaling pathway. This interaction promotes gemcitabine resistance by reducing DNA damage and inhibiting apoptosis. AKT inhibitor MK-2206 combined with gemcitabine reversed RRP9-overexpression-induced resistance. Immunoprecipitation (RRP9–IGF2BP1 interaction), immunofluorescence co-localization, RRP9 overexpression/siRNA knockdown, MTT assay, colony formation, FACS apoptosis, subcutaneous xenograft model Cell Communication and Signaling Medium 36434608
2024 RRP9 interacts with JUN protein; RRP9 deletion decreases JUN protein stability by accelerating JUN ubiquitination via MDM2, leading to JUN degradation. Loss of JUN or AKT pathway activation (SC79) attenuated the regulatory effects of RRP9 on breast cancer cell phenotypes. Co-immunoprecipitation (RRP9–JUN), protein stability assay, ubiquitination assay, gene expression array (prime-view), shRNA knockdown, rescue experiments Biology Direct Medium 39702367
2025 RRP9 overexpression activates the AKT signaling pathway in prostate cancer, resulting in phosphorylation of GSK3β at Ser9, which prevents β-catenin degradation and promotes cell metastasis, invasion, and EMT. AKT activator SC79 reversed the inhibitory effects of RRP9 knockdown. RRP9 overexpression/knockdown, western blot for AKT/GSK3β/β-catenin phosphorylation, rescue experiments with SC79, Transwell invasion/migration assays Discover Oncology Low 40526312
2025 RRP9 interacts with the scaffolding protein SQSTM1 (p62) in prostate cancer cells, identified by FLAG-RRP9 pull-down followed by MALDI-TOF/TOF mass spectrometry and validated by co-immunoprecipitation. SQSTM1 overexpression rescued the anti-growth and anti-migration effects of RRP9 knockdown. FLAG-RRP9 pull-down, MALDI-TOF/TOF mass spectrometry, co-immunoprecipitation, shRNA knockdown, rescue experiments, in vivo xenograft Advanced Biology Medium 40994061
2025 MYC transcriptionally regulates RRP9 expression. RRP9 knockdown impairs rRNA synthesis, reduces nucleolar size, and diminishes protein production in AML cells. Overexpression of RRP9 promotes AML cell proliferation and resistance to chidamide–cytarabine combination treatment. Transcriptomic analysis, binding assays (surface plasmon resonance for chidamide–MYC), RRP9 knockdown/overexpression, functional rRNA synthesis assays, nucleolar size measurement Cell Death & Disease Medium 40781078
2025 RRP9 promotes esophageal squamous cell carcinoma progression by enhancing E2F1-mediated transcriptional regulation of CDK1. RRP9 depletion reduced CDK1 expression and cell cycle progression. RRP9 knockdown/overexpression, luciferase or transcription reporter assays (E2F1-CDK1 axis implied), in vitro and in vivo functional assays Advanced Biology Low 40937881
2025 METTL1 promotes RRP9 mRNA stability through N7-methylguanosine (m7G) modification of RRP9 mRNA, as demonstrated by MeRIP assay and actinomycin D mRNA stability assay. This stabilization activates PI3K/AKT signaling via RRP9. MeRIP (methylated immunoprecipitation) assay, actinomycin D mRNA stability assay, METTL1 knockdown/overexpression, western blot for AKT pathway Molecular Carcinogenesis Medium 39960239
2026 RRP9 suppresses hepatocellular carcinoma by inhibiting the PI3K/AKT/mTOR pathway and downregulating cyclin A2 (CCNA2). Protein-protein interaction analysis and western blot identified an association between RRP9 and CCNA2; rescue experiments with PI3K activator 740Y-P and inhibitor PI3K/AKT/mTOR-IN-2 confirmed pathway involvement. Lentiviral KD/OE cell models, transcriptome sequencing, western blot, protein-protein interaction analysis, functional rescue with PI3K modulators, subcutaneous tumorigenesis in mice International Journal of Oncology Low 41952494

Source papers

Stage 0 corpus · 17 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2016 SIRT7-dependent deacetylation of the U3-55k protein controls pre-rRNA processing. Nature communications 114 26867678
2022 RRP9 promotes gemcitabine resistance in pancreatic cancer via activating AKT signaling pathway. Cell communication and signaling : CCS 39 36434608
2000 Interaction of the U3-55k protein with U3 snoRNA is mediated by the box B/C motif of U3 and the WD repeats of U3-55k. Nucleic acids research 38 10982864
2013 Structural and functional analysis of the U3 snoRNA binding protein Rrp9. RNA (New York, N.Y.) 26 23509373
2021 Neddylation modification of the U3 snoRNA-binding protein RRP9 by Smurf1 promotes tumorigenesis. The Journal of biological chemistry 25 34662580
2020 Synergistic defects in pre-rRNA processing from mutations in the U3-specific protein Rrp9 and U3 snoRNA. Nucleic acids research 22 31996908
2002 Cloning and expression of PARP-3 (Adprt3) and U3-55k, two genes closely linked on mouse chromosome 9. Folia biologica 13 12448766
2024 Regulation of microglia inflammation and oligodendrocyte demyelination by Engeletin via the TLR4/RRP9/NF-κB pathway after spinal cord injury. Pharmacological research 10 39395773
2025 METTL1 Enhances RRP9 mRNA Stability Through m7G Modification to Drive Colorectal Tumorigenesis. Molecular carcinogenesis 9 39960239
2024 The RRP9-JUN axis promotes breast cancer progression via the AKT signalling pathway. Biology direct 6 39702367
2023 RRP9 and DDX21 as new biomarkers of colorectal cancer. Medicine 4 37904456
2023 Joint effect of RRP9 and DDX21 on development of colorectal cancer and keloid. Aging 3 37988222
2025 Chidamide and cytarabine synergistically treat acute myeloid leukemia: inhibiting ribosome biogenesis via the MYC-RRP9 pathway. Cell death & disease 1 40781078
2025 RRP9 Promotes Esophageal Squamous Cell Carcinoma Progression through E2F1 Transcriptional Regulation of CDK1. Advanced biology 1 40937881
2026 RRP9 suppresses hepatocellular carcinoma progression by inhibiting the PI3K/AKT/mTOR pathway. International journal of oncology 0 41952494
2025 RRP9 promotes prostate cancer metastasis and epithelial-mesenchymal transition through activation of the AKT/GSK3β/β-Catenin signaling pathway. Discover oncology 0 40526312
2025 snoRNP RRP9 Promotes Prostate Cancer Cell Proliferation and Migration via SQSTM1. Advanced biology 0 40994061

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