Affinage

RPS25

Small ribosomal subunit protein eS25 · UniProt P62851

Length
125 aa
Mass
13.7 kDa
Annotated
2026-06-10
33 papers in source corpus 18 papers cited in narrative 18 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RPS25 (eS25) is a surface-exposed protein of the 40S ribosomal subunit that specifically enables non-canonical translation initiation while being dispensable for cap-dependent translation (PMID:19952110, PMID:23275440). It is positioned on the highly exposed face of the 40S subunit in close contact with other small-subunit proteins, contributing to subunit conformational stability (PMID:3378620). RPS25 directly contacts the conserved loop of the dicistroviral IGR-IRES, and purified 40S subunits lacking it cannot bind the IRES, establishing it as the key 40S determinant for IRES recognition (PMID:17287295, PMID:19952110); kinetic analysis shows it governs both the initial 40S-IRES binding step and the subsequent unimolecular conformational change that stabilizes the complex (PMID:32609821). This requirement extends across diverse non-canonical initiation modes, including the CrPV IGR, HCV, HIV-1, poliovirus IRESes and adenoviral ribosome shunting, so that loss of RPS25 selectively impairs amplification of viruses using these strategies (PMID:19952110, PMID:23275440, PMID:27191820). RPS25 is likewise required for repeat-associated non-AUG (RAN) translation of C9orf72 and FMR1 repeat expansions, and its depletion reduces production of toxic dipeptide and FMRpolyG proteins (PMID:31358992, PMID:40377206). Beyond translation, RPS25 binds MDM2 to inhibit its E3 ubiquitin ligase activity, forming a ternary complex with p53 that stabilizes p53; p53 in turn transcriptionally represses RPS25, creating a feedback loop, and RPS25 mRNA undergoes stress-induced nuclear retention controlled by p53, MTF-1 and La (PMID:22777350, PMID:11741912, PMID:8144559). RPS25 also functions in cell cycle progression and in Drosophila spermatogenesis (PMID:40045781, PMID:38341921).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 1988 Medium

    Established the physical position of RPS25 on the ribosome, showing it is a surface-exposed 40S protein whose integrity stabilizes subunit conformation — a structural prerequisite for later functional contacts.

    Evidence Immobilized trypsin digestion of rat liver 40S subunits with electric birefringence to assess conformation

    PMID:3378620

    Open questions at the time
    • No atomic-resolution placement of RPS25 within the 40S
    • Functional role beyond conformational stabilization not addressed
  2. 1994 Medium

    Revealed an unusual post-transcriptional control of RPS25 itself, with amino-acid deprivation inducing its mRNA but retaining it in the nucleus until nutrients return, decoupling transcription from translation.

    Evidence Northern blot, nuclear run-off, and nuclear/cytoplasmic/polysomal RNA fractionation under amino-acid deprivation in mammalian cells

    PMID:8144559

    Open questions at the time
    • Trans-acting factors mediating nuclear retention not identified
    • Physiological purpose of retention unresolved
  3. 1999 Medium

    Defined the targeting signals that route RPS25 to the nucleolus, mapping an N-terminal basic stretch sufficient for nuclear/nucleolar import in human cells and an overlapping novel-class NLS in yeast.

    Evidence Epitope-tagged deletion/site-directed mutants in Cos-1 cells with immunofluorescence; mutational NLS analysis in yeast

    PMID:10050887 PMID:10386617

    Open questions at the time
    • Import receptors not identified
    • Relationship to ribosome assembly route not defined
  4. 2001 Medium

    Identified the trans-acting factors (p53, MTF-1, La) controlling stress-induced nuclear export of RPS25 mRNA, linking its regulation to a p53-mediated apoptotic pathway.

    Evidence Nuclear/cytoplasmic RNA fractionation and protein-interaction studies in hepatoma cells under nutrient deprivation

    PMID:11741912

    Open questions at the time
    • Direct RNA-binding mechanism of each factor not fully resolved
    • Generality beyond hepatoma cells untested
  5. 2007 High

    Pinpointed a direct RPS25-IRES contact, showing RPS25 crosslinks to a conserved loop of the dicistroviral IGR-IRES with no contact to 18S rRNA, establishing it as the physical interface for IRES recognition.

    Evidence 4-thiouridine crosslinking of the IGR-IRES to 40S proteins with site-directed IRES mutagenesis

    PMID:17287295

    Open questions at the time
    • Did not test functional requirement of the contact
    • Structural geometry of the interface unknown
  6. 2009 High

    Demonstrated RPS25 is specifically and functionally required for IRES-mediated initiation but dispensable for cap-dependent translation, using genetic deletion and in vitro reconstitution.

    Evidence Yeast deletion strains, in vitro 40S-IRES binding with purified Rps25-lacking 40S, and mammalian reporter assays

    PMID:19952110

    Open questions at the time
    • Mechanistic basis for selective IRES dependence not fully explained
    • Comparative analysis of bacterial S20p counterpart at this stage was computational only (2009, PMID 20034956, Low)
  7. 2012 High

    Extended the RPS25 requirement to ribosome shunting and revealed a parallel non-ribosomal role as an MDM2 inhibitor and p53 stabilizer, uncovering both a shared non-canonical initiation mechanism and a feedback loop with p53.

    Evidence siRNA knockdown with multi-virus amplification assays; Co-IP, ubiquitination, ChIP, and domain-mapping for the MDM2/p53 axis

    PMID:22777350 PMID:23275440

    Open questions at the time
    • Whether MDM2 binding is by free RPS25 or ribosome-bound RPS25 not resolved
    • Structural basis of MDM2 inhibition unknown
  8. 2016 Medium

    Showed RPS25 is required for HIV-1 IRES activity and that 40S recruitment proceeds without scanning, broadening the range of viral IRESes dependent on RPS25.

    Evidence siRNA knockdown and HIV-1 IRES reporter assays with mutational dissection of the 5' leader

    PMID:27191820

    Open questions at the time
    • Direct RPS25-HIV-1 IRES contact not mapped
    • Mechanism of scanning-independent initiation not defined
  9. 2019 High

    Established RPS25 as a requirement for RAN translation of C9orf72 repeat expansions, connecting non-canonical initiation to neurodegenerative dipeptide-repeat toxicity.

    Evidence Genetic screen for RAN translation regulators validated in yeast, mammalian cells, and Drosophila

    PMID:31358992

    Open questions at the time
    • Whether RPS25 contacts repeat RNA directly not shown
    • Therapeutic tractability of targeting RPS25 unaddressed
  10. 2020 High

    Dissected the two-step kinetics of 40S-IRES complex assembly and a stable cell-state transition upon RPS25 loss, deepening the mechanistic and phenotypic understanding of RPS25 function.

    Evidence Kinetic in vitro binding with eS25 mutagenesis; CRISPR knockout with cDNA rescue, genomic repair, and transcriptomics

    PMID:32463448 PMID:32609821

    Open questions at the time
    • Molecular basis of the non-rescuable cell-state transition unknown
    • Structural model of the eS25 mutation effects on conformational change lacking
  11. 2025 Medium

    Revealed translation-independent roles of RPS25 in cell cycle progression and additional RAN-translation substrates, expanding its functional repertoire beyond viral IRESes.

    Evidence siRNA knockdown with flow-cytometric cell cycle analysis and BKPyV assays; RAN translation reporters for FMR1 CGG repeats

    PMID:40045781 PMID:40377206

    Open questions at the time
    • Mechanism coupling RPS25 to cell cycle control unknown
    • Whether cell-cycle role is ribosome-dependent unresolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • How RPS25 mechanistically distinguishes non-canonical initiation events from cap-dependent translation at structural resolution, and how its ribosomal and extra-ribosomal (MDM2/p53, cell cycle, spermatogenesis) functions are coordinated, remains unresolved.
  • No high-resolution structure of RPS25 engaging an IRES or repeat RNA
  • Partition between ribosome-bound and free RPS25 pools across functions undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 3 GO:0045182 translation regulator activity 3 GO:0005198 structural molecule activity 1 GO:0098772 molecular function regulator activity 1
Localization
GO:0005634 nucleus 2 GO:0005730 nucleolus 2 GO:0005840 ribosome 2 GO:0005829 cytosol 1
Pathway
R-HSA-1643685 Disease 3
Partners
LA (SSB)MDM2MDMXMTF-1TP53
Complex memberships
40S ribosomal subunit

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 RPS25 (rpS25) directly contacts the conserved loop region (nucleotides UU6089-6090 in domain 2b) of the dicistroviral IGR-IRES, as demonstrated by chemical crosslinking with 4-thiouridine-labeled IRES; rpS25 showed the strongest crosslinking signal among 40S proteins, and no crosslinking was detected to 18S rRNA. Chemical crosslinking with 4-thiouridine-labeled IGR-IRES; site-directed mutagenesis of IRES nucleotides; identification of crosslinked proteins from 40S subunit Nucleic acids research High 17287295
2009 RPS25 is specifically required for IRES-mediated translation initiation by the CrPV IGR IRES and HCV IRES, but not for cap-dependent translation. Purified 40S ribosomal subunits lacking Rps25 are unable to bind to the IGR IRES in vitro. Loss of Rps25 causes only slight defects in global translation, ribosome biogenesis, readthrough, and programmed ribosomal frameshifting. Yeast genetics (deletion strains); in vitro 40S-IRES binding assay with purified 40S subunits lacking Rps25; mammalian cell reporter assays; ribosome biogenesis and frameshifting assays Genes & development High 19952110
2012 RPS25 is required not only for IRES-mediated translation initiation but also for ribosome shunting (as used by adenovirus), suggesting these two alternative initiation pathways share a common mechanism dependent on RPS25 that is distinct from cap-dependent translation. Viruses relying on IRES (HCV, poliovirus) or ribosome shunting (adenovirus) show impaired amplification in RPS25-depleted cells, while herpes simplex virus (cap-dependent) does not. siRNA knockdown of RPS25 in mammalian cells; viral amplification assays (HCV, poliovirus, adenovirus, HSV); reporter assays for cap-dependent vs. IRES/shunt-dependent translation Molecular and cellular biology High 23275440
2012 RPS25 interacts with MDM2 and inhibits its E3 ubiquitin ligase activity, leading to reduced MDM2-mediated p53 ubiquitination and stabilization/activation of p53. RPS25, MDM2, and p53 form a ternary complex following ribosomal stress. The nucleolar localization and MDM2-binding domains of RPS25 are required for this activity. RPS25 also stabilizes MDMX to cooperatively regulate MDM2 E3 ligase activity. p53 in turn transcriptionally suppresses RPS25 expression by directly binding the S25 promoter, forming a feedback loop. Co-immunoprecipitation; siRNA knockdown; ubiquitination assays; luciferase reporter assays; ChIP assay for p53 binding to S25 promoter; deletion/domain mapping mutants Oncogene High 22777350
1999 Human RPS25 localizes to the cell nucleus with strong predominance in the nucleolus. A 17-residue peptide at the amino terminus (second NOS-like basic stretch) is sufficient for nuclear and nucleolar targeting, as determined by deletion and site-directed mutagenesis of epitope-tagged RPS25 expressed in Cos-1 cells. Expression of epitope-tagged RPS25 in Cos-1 cells; immunofluorescence; deletion mutagenesis; site-directed mutagenesis; chimeric construct analysis Oncogene High 10050887
1999 In Saccharomyces cerevisiae, the nucleolar targeting information of ribosomal protein S25 overlaps with its nuclear localization sequence (NLS), and the NLS belongs to a novel ribosomal protein-specific class distinct from classical Chelsky and bipartite NLSs. Mutational analysis of yeast S25 NLS; nuclear/nucleolar localization assay in yeast FEBS letters Medium 10386617
2001 RPS25 mRNA is post-transcriptionally regulated by p53, MTF-1, and La, which control nuclear export of stress-induced S25 mRNA in hepatoma cells. Under nutrient deprivation, S25 mRNA is retained in the nucleus and exported to the cytosol only upon nutrient replenishment or after prolonged starvation, participating in a p53-mediated apoptotic pathway. Nuclear/cytoplasmic RNA fractionation; protein interaction studies; functional assays in hepatoma cells under nutrient deprivation; identification of MTF-1 and La as RPS25 mRNA-binding partners The Journal of biological chemistry Medium 11741912
1994 RPS25 (S25) mRNA is uniquely upregulated by amino acid deprivation at the transcriptional level, and the induced mRNA is retained in the nucleus (not available for translation) rather than being exported to the cytoplasm; nuclear retention is relieved by amino acid replenishment, at which point mRNA moves to the polysomal fraction. Northern blot analysis; nuclear run-off transcription assay; cytoplasmic/nuclear/polysomal RNA fractionation; actinomycin D and cycloheximide treatment The Journal of biological chemistry Medium 8144559
2016 The HIV-1 IRES activity requires RPS25 (eS25). Once the 40S subunit is recruited to the HIV-1 IRES, translation initiates without ribosome scanning. The IRES is modular in nature, with distinct structural domains contributing to 40S subunit recruitment. siRNA knockdown of RPS25 in mammalian cells; reporter assays for HIV-1 IRES activity; mutational analysis of HIV-1 5' leader structural domains The FEBS journal Medium 27191820
2019 RPS25 is required for efficient repeat-associated non-AUG (RAN) translation of C9orf72 nucleotide repeat expansions, generating dipeptide repeat proteins. Identified by genetic screen in yeast and validated in mammalian models and Drosophila. Genetic screen for regulators of RAN translation; validation in yeast, mammalian cells, and Drosophila models Nature neuroscience High 31358992
2020 Formation of a stable 40S-CrPV IGR IRES complex occurs in two successive steps: an initial fast binding step followed by a slow unimolecular conformational change that stabilizes the complex. RPS25 (eS25) impacts both steps: mutations in eS25 either decrease 40S-IRES complex formation or increase the rate of the conformational change, preventing proper stabilization. Kinetic binding studies (stopped-flow or equivalent); eS25 mutagenesis; 40S-IRES complex formation assays in vitro Nucleic acids research High 32609821
2020 Genetic knockout of RPS25 in human cells results in viral- and toxin-resistance phenotypes that cannot be rescued by re-expression of functional RPS25 cDNA, indicating that RPS25 loss drives a stable cell-state transition with pleiotropic phenotypic and gene expression changes that persist even after RPS25 expression is restored by genomic locus repair. CRISPR knockout of RPS25 in human cell lines; viral infection resistance assays; toxin resistance assays; cDNA rescue experiments; genomic locus repair; transcriptome analysis Nucleic acids research Medium 32463448
2017 HTLV-1 HBZ induces nuclear retention of RPS25 mRNA and loss of RPS25 protein expression, which bypasses translational control of the JunD upstream open reading frame (uORF) and favors expression of the truncated ΔJunD isoform that promotes proliferation and transformation. RPS25 mRNA nuclear retention assay; Western blot for RPS25 protein; luciferase reporter assays for JunD uORF translation; functional assays for ΔJunD in cell proliferation and transformation; various cell lines and primary T-lymphocytes Leukemia Medium 28260789
1988 RPS25 is located on the surface of the mammalian 40S ribosomal subunit, is highly exposed and in close physical contact with ribosomal proteins S2, S6, S10, S14, and S15. Digestion of these surface-exposed proteins by immobilized trypsin causes unfolding of 40S subunits, indicating these proteins stabilize subunit conformation. Immobilized trypsin digestion of rat liver 40S subunits; protein identification by gel electrophoresis; electric birefringence to assess subunit conformation FEBS letters Medium 3378620
2009 The conserved structural motifs of bacterial ribosomal protein S20p that contact rRNA are present in eukaryotic ribosomal protein S25e (RPS25), establishing RPS25 as the eukaryotic functional counterpart of bacterial S20p for rRNA-contacting structural motifs. Comparative sequence alignment of bacterial and eukaryotic ribosomal proteins; analysis of rRNA contact residues from Thermus thermophilus 30S crystal structure Nucleic acids research Low 20034956
2025 RPS25 knockdown in primary kidney cells decreases the proportion of cycling cells, causing arrest at both G0/G1 and G2/M phases. This cell cycle arrest reduces productive BK polyomavirus infection, revealing a role for eS25 in cell cycle control independent of its role in alternative translation initiation. siRNA knockdown of eS25 in primary kidney cells; cell cycle analysis by flow cytometry; viral production assays for BKPyV Philosophical transactions of the Royal Society of London. Series B, Biological sciences Medium 40045781
2025 Depletion of RPS25 (in addition to RPS26) suppresses RAN translation of CGG repeat-expanded FMR1 mRNA, reducing production of the toxic FMRpolyG protein in fragile X premutation-associated conditions. siRNA knockdown of RPS25 in mammalian cells; reporter assays for FMRpolyG RAN translation; toxicity assays eLife Medium 40377206
2024 RpS25 is required for spermatid elongation and individualization during Drosophila spermatogenesis. Knockdown causes shortened cyst elongation, disrupted spermatid nuclei bundling, and failure of individualization complex assembly from actin cones, resulting in male sterility. RNAi knockdown of RpS25 in Drosophila testes; microscopic examination of spermatogenesis stages; actin cone and individualization complex assembly assays Biochemical and biophysical research communications Medium 38341921

Source papers

Stage 0 corpus · 33 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2009 RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs. Genes & development 169 19952110
2012 Ribosomal protein S25 dependency reveals a common mechanism for diverse internal ribosome entry sites and ribosome shunting. Molecular and cellular biology 95 23275440
2019 RPS25 is required for efficient RAN translation of C9orf72 and other neurodegenerative disease-associated nucleotide repeats. Nature neuroscience 82 31358992
2012 Identification of ribosomal protein S25 (RPS25)-MDM2-p53 regulatory feedback loop. Oncogene 79 22777350
2016 Reduction of selenite to Se(0) nanoparticles by filamentous bacterium Streptomyces sp. ES2-5 isolated from a selenium mining soil. Microbial cell factories 62 27630128
2007 Eukaryotic ribosomal protein RPS25 interacts with the conserved loop region in a dicistroviral intergenic internal ribosome entry site. Nucleic acids research 60 17287295
2001 Ribosomal protein S25 mRNA partners with MTF-1 and La to provide a p53-mediated mechanism for survival or death. The Journal of biological chemistry 38 11741912
1999 Nuclear and nucleolar targeting of human ribosomal protein S25: common features shared with HIV-1 regulatory proteins. Oncogene 38 10050887
1994 Nuclear retention of the induced mRNA following amino acid-dependent transcriptional regulation of mammalian ribosomal proteins L17 and S25. The Journal of biological chemistry 36 8144559
2016 Structural domains within the HIV-1 mRNA and the ribosomal protein S25 influence cap-independent translation initiation. The FEBS journal 32 27191820
2019 Glutaredoxin S25 and its interacting TGACG motif-binding factor TGA2 mediate brassinosteroid-induced chlorothalonil metabolism in tomato plants. Environmental pollution (Barking, Essex : 1987) 31 31563783
1999 Nuclear and nucleolar localization of Saccharomyces cerevisiae ribosomal proteins S22 and S25. FEBS letters 26 10386617
2017 HBZ-mediated shift of JunD from growth suppressor to tumor promoter in leukemic cells by inhibition of ribosomal protein S25 expression. Leukemia 24 28260789
1988 Ribosomal proteins S2, S6, S10, S14, S15 and S25 are localized on the surface of mammalian 40 S subunits and stabilize their conformation. A study with immobilized trypsin. FEBS letters 18 3378620
1980 Purification of Drosophila ribosomal proteins. Isolation of proteins S8, S13, S14, S16, S19, S20/L24, S22/L26, S24, S25/S27, S26, S29, L4, L10/L11, L12, L13, L16, L18, L19, L27, 1, 7/8, 9, and 11. Biochemistry 16 6773542
1992 Regulation of ribosomal protein S25 in HL60 cells isolated for resistance to adriamycin. FEBS letters 13 1544436
1984 Immunological evidence for structural homology between Drosophila melanogaster (S14), rabbit liver (S12), Saccharomyces cerevisiae (S25), Bacillus subtilis (S6), and Escherichia coli (S6) ribosomal proteins. Molecular and cellular biology 13 6083442
2020 Binding of a viral IRES to the 40S subunit occurs in two successive steps mediated by eS25. Nucleic acids research 12 32609821
1991 Cloning and sequencing a cDNA encoding human ribosomal protein S25. Gene 12 1748303
2020 A memory of eS25 loss drives resistance phenotypes. Nucleic acids research 10 32463448
2009 Structural motifs of the bacterial ribosomal proteins S20, S18 and S16 that contact rRNA present in the eukaryotic ribosomal proteins S25, S26 and S27A, respectively. Nucleic acids research 9 20034956
2002 Increased expression of the S25 ribosomal protein gene occurs during ageing of the rat liver. Gerontology 9 12393952
1987 Esterase-25 (Es-25): identification and characterization of a new kidney arylesterase of the house mouse, genetically linked to Ly-18 on chromosome 12. Biochemical genetics 7 3481261
2019 Comparative genomics analysis of Raoultella planticola S25 isolated from duck in China, with florfenicol resistance. Comparative immunology, microbiology and infectious diseases 6 31775114
2025 Insufficiency of 40S ribosomal proteins, RPS26 and RPS25, negatively affects biosynthesis of polyglycine-containing proteins in fragile-X associated conditions. eLife 5 40377206
2024 RpS25 is required for sperm elongation and individualization during Drosophila spermatogenesis. Biochemical and biophysical research communications 5 38341921
2017 Genetic characterization and fine mapping of S25, a hybrid male sterility gene, on rice chromosome 12. Genes & genetic systems 5 28674278
2025 Ribosomal protein S25 promotes cell cycle entry for a productive BK polyomavirus infection. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 4 40045781
1998 Quantification of human lithostathine S2-5 forms using the antibody to the N-terminal peptide region. Pancreas 4 9598807
2019 Subtle Changes in the Combining Site of the Chlamydiaceae-Specific mAb S25-23 Increase the Antibody-Carbohydrate Binding Affinity by an Order of Magnitude. Biochemistry 3 30571096
2008 cDNA, genomic sequence cloning and overexpression of ribosomal protein S25 gene (RPS25) from the Giant Panda. Molecular biology reports 2 19101821
1992 The primary structure of rat ribosomal protein S25. Biochemical and biophysical research communications 2 1354961
1995 Excess expression of uterine ribosomal protein genes P2 and S25 during the "implantation window" in the rat. Journal of the Society for Gynecologic Investigation 1 9420878

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