{"gene":"RPS25","run_date":"2026-06-10T07:46:27","timeline":{"discoveries":[{"year":2007,"finding":"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.","method":"Chemical crosslinking with 4-thiouridine-labeled IGR-IRES; site-directed mutagenesis of IRES nucleotides; identification of crosslinked proteins from 40S subunit","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct in vitro crosslinking with site-directed mutagenesis to map the contact site, single lab but two orthogonal methods","pmids":["17287295"],"is_preprint":false},{"year":2009,"finding":"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.","method":"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","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with purified components, genetic deletion in yeast, validated in mammalian cells, multiple orthogonal methods","pmids":["19952110"],"is_preprint":false},{"year":2012,"finding":"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.","method":"siRNA knockdown of RPS25 in mammalian cells; viral amplification assays (HCV, poliovirus, adenovirus, HSV); reporter assays for cap-dependent vs. IRES/shunt-dependent translation","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal functional assays across multiple viral systems, siRNA depletion with multiple readouts, replicates prior finding with new pathway","pmids":["23275440"],"is_preprint":false},{"year":2012,"finding":"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.","method":"Co-immunoprecipitation; siRNA knockdown; ubiquitination assays; luciferase reporter assays; ChIP assay for p53 binding to S25 promoter; deletion/domain mapping mutants","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 / Moderate — co-IP, ubiquitination assay, ChIP, and domain mapping in single lab with multiple orthogonal methods","pmids":["22777350"],"is_preprint":false},{"year":1999,"finding":"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.","method":"Expression of epitope-tagged RPS25 in Cos-1 cells; immunofluorescence; deletion mutagenesis; site-directed mutagenesis; chimeric construct analysis","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 / Moderate — direct localization with deletion and site-directed mutagenesis defining the targeting signal, functional consequence mapped","pmids":["10050887"],"is_preprint":false},{"year":1999,"finding":"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.","method":"Mutational analysis of yeast S25 NLS; nuclear/nucleolar localization assay in yeast","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — mutational analysis in yeast, single lab, single method described","pmids":["10386617"],"is_preprint":false},{"year":2001,"finding":"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.","method":"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","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNA fractionation and protein-binding assays in single lab with multiple methods","pmids":["11741912"],"is_preprint":false},{"year":1994,"finding":"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.","method":"Northern blot analysis; nuclear run-off transcription assay; cytoplasmic/nuclear/polysomal RNA fractionation; actinomycin D and cycloheximide treatment","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — nuclear run-off plus fractionation with multiple pharmacological controls, single lab","pmids":["8144559"],"is_preprint":false},{"year":2016,"finding":"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.","method":"siRNA knockdown of RPS25 in mammalian cells; reporter assays for HIV-1 IRES activity; mutational analysis of HIV-1 5' leader structural domains","journal":"The FEBS journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA knockdown with reporter assays and mutational analysis of IRES, single lab","pmids":["27191820"],"is_preprint":false},{"year":2019,"finding":"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.","method":"Genetic screen for regulators of RAN translation; validation in yeast, mammalian cells, and Drosophila models","journal":"Nature neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic screen plus multi-organism validation (yeast, mammalian, Drosophila), multiple orthogonal approaches","pmids":["31358992"],"is_preprint":false},{"year":2020,"finding":"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.","method":"Kinetic binding studies (stopped-flow or equivalent); eS25 mutagenesis; 40S-IRES complex formation assays in vitro","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro kinetic reconstitution with mutagenesis defining mechanistic steps, single lab","pmids":["32609821"],"is_preprint":false},{"year":2020,"finding":"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.","method":"CRISPR knockout of RPS25 in human cell lines; viral infection resistance assays; toxin resistance assays; cDNA rescue experiments; genomic locus repair; transcriptome analysis","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple knockout clones, rescue experiments, genomic repair, transcriptomics, single lab","pmids":["32463448"],"is_preprint":false},{"year":2017,"finding":"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.","method":"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","journal":"Leukemia","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mRNA fractionation, protein expression, reporter assays, and functional readout, single lab with multiple methods","pmids":["28260789"],"is_preprint":false},{"year":1988,"finding":"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.","method":"Immobilized trypsin digestion of rat liver 40S subunits; protein identification by gel electrophoresis; electric birefringence to assess subunit conformation","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct biochemical localization with functional consequence (unfolding), single study","pmids":["3378620"],"is_preprint":false},{"year":2009,"finding":"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.","method":"Comparative sequence alignment of bacterial and eukaryotic ribosomal proteins; analysis of rRNA contact residues from Thermus thermophilus 30S crystal structure","journal":"Nucleic acids research","confidence":"Low","confidence_rationale":"Tier 4 / Moderate — computational/comparative analysis, no direct experimental validation of rRNA contacts for eukaryotic S25","pmids":["20034956"],"is_preprint":false},{"year":2025,"finding":"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.","method":"siRNA knockdown of eS25 in primary kidney cells; cell cycle analysis by flow cytometry; viral production assays for BKPyV","journal":"Philosophical transactions of the Royal Society of London. Series B, Biological sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — knockdown with cell cycle flow cytometry and viral production assay, single lab with two readouts","pmids":["40045781"],"is_preprint":false},{"year":2025,"finding":"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.","method":"siRNA knockdown of RPS25 in mammalian cells; reporter assays for FMRpolyG RAN translation; toxicity assays","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA knockdown with functional RAN translation reporters, single lab, corroborates prior finding on RAN translation","pmids":["40377206"],"is_preprint":false},{"year":2024,"finding":"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.","method":"RNAi knockdown of RpS25 in Drosophila testes; microscopic examination of spermatogenesis stages; actin cone and individualization complex assembly assays","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — tissue-specific knockdown in Drosophila with defined cellular phenotypes at multiple spermatogenesis stages, single lab","pmids":["38341921"],"is_preprint":false}],"current_model":"RPS25 (eS25) is a surface-exposed protein of the 40S ribosomal subunit that directly contacts IRES RNA elements to mediate both initial binding and conformational stabilization of the 40S-IRES complex, making it specifically required for multiple non-canonical translation initiation mechanisms—including IRES-mediated initiation (CrPV IGR, HCV, HIV-1, poliovirus), ribosome shunting, and RAN translation—while being dispensable for cap-dependent translation; in addition, RPS25 interacts with MDM2 to inhibit its E3 ligase activity and stabilize p53 (forming a feedback loop where p53 represses RPS25 transcription), its mRNA undergoes stress-induced nuclear retention controlled by p53/MTF-1/La, and it plays roles in cell cycle progression and spermatogenesis."},"narrative":{"mechanistic_narrative":"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].","teleology":[{"year":1988,"claim":"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","pmids":["3378620"],"confidence":"Medium","gaps":["No atomic-resolution placement of RPS25 within the 40S","Functional role beyond conformational stabilization not addressed"]},{"year":1994,"claim":"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","pmids":["8144559"],"confidence":"Medium","gaps":["Trans-acting factors mediating nuclear retention not identified","Physiological purpose of retention unresolved"]},{"year":1999,"claim":"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","pmids":["10050887","10386617"],"confidence":"Medium","gaps":["Import receptors not identified","Relationship to ribosome assembly route not defined"]},{"year":2001,"claim":"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","pmids":["11741912"],"confidence":"Medium","gaps":["Direct RNA-binding mechanism of each factor not fully resolved","Generality beyond hepatoma cells untested"]},{"year":2007,"claim":"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","pmids":["17287295"],"confidence":"High","gaps":["Did not test functional requirement of the contact","Structural geometry of the interface unknown"]},{"year":2009,"claim":"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","pmids":["19952110"],"confidence":"High","gaps":["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)"]},{"year":2012,"claim":"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","pmids":["23275440","22777350"],"confidence":"High","gaps":["Whether MDM2 binding is by free RPS25 or ribosome-bound RPS25 not resolved","Structural basis of MDM2 inhibition unknown"]},{"year":2016,"claim":"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","pmids":["27191820"],"confidence":"Medium","gaps":["Direct RPS25-HIV-1 IRES contact not mapped","Mechanism of scanning-independent initiation not defined"]},{"year":2019,"claim":"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","pmids":["31358992"],"confidence":"High","gaps":["Whether RPS25 contacts repeat RNA directly not shown","Therapeutic tractability of targeting RPS25 unaddressed"]},{"year":2020,"claim":"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","pmids":["32609821","32463448"],"confidence":"High","gaps":["Molecular basis of the non-rescuable cell-state transition unknown","Structural model of the eS25 mutation effects on conformational change lacking"]},{"year":2025,"claim":"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","pmids":["40045781","40377206"],"confidence":"Medium","gaps":["Mechanism coupling RPS25 to cell cycle control unknown","Whether cell-cycle role is ribosome-dependent unresolved"]},{"year":null,"claim":"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.","evidence":"","pmids":[],"confidence":"Medium","gaps":["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":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1,10]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[13]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[1,2,9]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[3,4]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[4,7]},{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[13,1]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[2,8,9]}],"complexes":["40S ribosomal subunit"],"partners":["MDM2","MDMX","TP53","MTF-1","LA (SSB)"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P62851","full_name":"Small ribosomal subunit protein eS25","aliases":["40S ribosomal protein S25"],"length_aa":125,"mass_kda":13.7,"function":"Component of the small ribosomal subunit (PubMed:23636399). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:23636399)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P62851/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPS25","classification":"Common Essential","n_dependent_lines":1202,"n_total_lines":1208,"dependency_fraction":0.9950331125827815},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPRIN1","stoichiometry":10.0},{"gene":"EIF2S3","stoichiometry":10.0},{"gene":"EIF3B","stoichiometry":10.0},{"gene":"ENY2","stoichiometry":10.0},{"gene":"GSPT1","stoichiometry":10.0},{"gene":"METAP2","stoichiometry":10.0},{"gene":"NCAPH","stoichiometry":10.0},{"gene":"RACK1","stoichiometry":10.0},{"gene":"RBM8A","stoichiometry":10.0},{"gene":"RPL11","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/RPS25","total_profiled":1310},"omim":[{"mim_id":"180465","title":"RIBOSOMAL PROTEIN S25; RPS25","url":"https://www.omim.org/entry/180465"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Endoplasmic reticulum","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"},{"location":"Nucleoli","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPS25"},"hgnc":{"alias_symbol":["S25","eS25"],"prev_symbol":[]},"alphafold":{"accession":"P62851","domains":[{"cath_id":"1.10.10.10","chopping":"51-110","consensus_level":"high","plddt":89.992,"start":51,"end":110}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P62851","model_url":"https://alphafold.ebi.ac.uk/files/AF-P62851-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P62851-F1-predicted_aligned_error_v6.png","plddt_mean":73.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPS25","jax_strain_url":"https://www.jax.org/strain/search?query=RPS25"},"sequence":{"accession":"P62851","fasta_url":"https://rest.uniprot.org/uniprotkb/P62851.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P62851/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P62851"}},"corpus_meta":[{"pmid":"19952110","id":"PMC_19952110","title":"RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs.","date":"2009","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/19952110","citation_count":169,"is_preprint":false},{"pmid":"23275440","id":"PMC_23275440","title":"Ribosomal protein S25 dependency reveals a common mechanism for diverse internal ribosome entry sites and ribosome shunting.","date":"2012","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/23275440","citation_count":95,"is_preprint":false},{"pmid":"31358992","id":"PMC_31358992","title":"RPS25 is required for efficient RAN translation of C9orf72 and other neurodegenerative disease-associated nucleotide repeats.","date":"2019","source":"Nature neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/31358992","citation_count":82,"is_preprint":false},{"pmid":"22777350","id":"PMC_22777350","title":"Identification of ribosomal protein S25 (RPS25)-MDM2-p53 regulatory feedback loop.","date":"2012","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/22777350","citation_count":79,"is_preprint":false},{"pmid":"27630128","id":"PMC_27630128","title":"Reduction of selenite to Se(0) nanoparticles by filamentous bacterium Streptomyces sp. ES2-5 isolated from a selenium mining soil.","date":"2016","source":"Microbial cell factories","url":"https://pubmed.ncbi.nlm.nih.gov/27630128","citation_count":62,"is_preprint":false},{"pmid":"17287295","id":"PMC_17287295","title":"Eukaryotic ribosomal protein RPS25 interacts with the conserved loop region in a dicistroviral intergenic internal ribosome entry site.","date":"2007","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/17287295","citation_count":60,"is_preprint":false},{"pmid":"10050887","id":"PMC_10050887","title":"Nuclear and nucleolar targeting of human ribosomal protein S25: common features shared with HIV-1 regulatory proteins.","date":"1999","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/10050887","citation_count":38,"is_preprint":false},{"pmid":"11741912","id":"PMC_11741912","title":"Ribosomal protein S25 mRNA partners with MTF-1 and La to provide a p53-mediated mechanism for survival or death.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11741912","citation_count":38,"is_preprint":false},{"pmid":"8144559","id":"PMC_8144559","title":"Nuclear retention of the induced mRNA following amino acid-dependent transcriptional regulation of mammalian ribosomal proteins L17 and S25.","date":"1994","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8144559","citation_count":36,"is_preprint":false},{"pmid":"27191820","id":"PMC_27191820","title":"Structural domains within the HIV-1 mRNA and the ribosomal protein S25 influence cap-independent translation initiation.","date":"2016","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/27191820","citation_count":32,"is_preprint":false},{"pmid":"31563783","id":"PMC_31563783","title":"Glutaredoxin S25 and its interacting TGACG motif-binding factor TGA2 mediate brassinosteroid-induced chlorothalonil metabolism in tomato plants.","date":"2019","source":"Environmental pollution (Barking, Essex : 1987)","url":"https://pubmed.ncbi.nlm.nih.gov/31563783","citation_count":31,"is_preprint":false},{"pmid":"10386617","id":"PMC_10386617","title":"Nuclear and nucleolar localization of Saccharomyces cerevisiae ribosomal proteins S22 and S25.","date":"1999","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/10386617","citation_count":26,"is_preprint":false},{"pmid":"28260789","id":"PMC_28260789","title":"HBZ-mediated shift of JunD from growth suppressor to tumor promoter in leukemic cells by inhibition of ribosomal protein S25 expression.","date":"2017","source":"Leukemia","url":"https://pubmed.ncbi.nlm.nih.gov/28260789","citation_count":24,"is_preprint":false},{"pmid":"3378620","id":"PMC_3378620","title":"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.","date":"1988","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/3378620","citation_count":18,"is_preprint":false},{"pmid":"6773542","id":"PMC_6773542","title":"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.","date":"1980","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/6773542","citation_count":16,"is_preprint":false},{"pmid":"1544436","id":"PMC_1544436","title":"Regulation of ribosomal protein S25 in HL60 cells isolated for resistance to adriamycin.","date":"1992","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/1544436","citation_count":13,"is_preprint":false},{"pmid":"6083442","id":"PMC_6083442","title":"Immunological evidence for structural homology between Drosophila melanogaster (S14), rabbit liver (S12), Saccharomyces cerevisiae (S25), Bacillus subtilis (S6), and Escherichia coli (S6) ribosomal proteins.","date":"1984","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/6083442","citation_count":13,"is_preprint":false},{"pmid":"32609821","id":"PMC_32609821","title":"Binding of a viral IRES to the 40S subunit occurs in two successive steps mediated by eS25.","date":"2020","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/32609821","citation_count":12,"is_preprint":false},{"pmid":"1748303","id":"PMC_1748303","title":"Cloning and sequencing a cDNA encoding human ribosomal protein S25.","date":"1991","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/1748303","citation_count":12,"is_preprint":false},{"pmid":"32463448","id":"PMC_32463448","title":"A memory of eS25 loss drives resistance phenotypes.","date":"2020","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/32463448","citation_count":10,"is_preprint":false},{"pmid":"12393952","id":"PMC_12393952","title":"Increased expression of the S25 ribosomal protein gene occurs during ageing of the rat liver.","date":"2002","source":"Gerontology","url":"https://pubmed.ncbi.nlm.nih.gov/12393952","citation_count":9,"is_preprint":false},{"pmid":"20034956","id":"PMC_20034956","title":"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.","date":"2009","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/20034956","citation_count":9,"is_preprint":false},{"pmid":"3481261","id":"PMC_3481261","title":"Esterase-25 (Es-25): identification and characterization of a new kidney arylesterase of the house mouse, genetically linked to Ly-18 on chromosome 12.","date":"1987","source":"Biochemical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/3481261","citation_count":7,"is_preprint":false},{"pmid":"31775114","id":"PMC_31775114","title":"Comparative genomics analysis of Raoultella planticola S25 isolated from duck in China, with florfenicol resistance.","date":"2019","source":"Comparative immunology, microbiology and infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/31775114","citation_count":6,"is_preprint":false},{"pmid":"38341921","id":"PMC_38341921","title":"RpS25 is required for sperm elongation and individualization during Drosophila spermatogenesis.","date":"2024","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/38341921","citation_count":5,"is_preprint":false},{"pmid":"40377206","id":"PMC_40377206","title":"Insufficiency of 40S ribosomal proteins, RPS26 and RPS25, negatively affects biosynthesis of polyglycine-containing proteins in fragile-X associated conditions.","date":"2025","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/40377206","citation_count":5,"is_preprint":false},{"pmid":"28674278","id":"PMC_28674278","title":"Genetic characterization and fine mapping of S25, a hybrid male sterility gene, on rice chromosome 12.","date":"2017","source":"Genes & genetic systems","url":"https://pubmed.ncbi.nlm.nih.gov/28674278","citation_count":5,"is_preprint":false},{"pmid":"40045781","id":"PMC_40045781","title":"Ribosomal protein S25 promotes cell cycle entry for a productive BK polyomavirus infection.","date":"2025","source":"Philosophical transactions of the Royal Society of London. 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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.\",\n      \"method\": \"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\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with purified components, genetic deletion in yeast, validated in mammalian cells, multiple orthogonal methods\",\n      \"pmids\": [\"19952110\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"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.\",\n      \"method\": \"siRNA knockdown of RPS25 in mammalian cells; viral amplification assays (HCV, poliovirus, adenovirus, HSV); reporter assays for cap-dependent vs. IRES/shunt-dependent translation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal functional assays across multiple viral systems, siRNA depletion with multiple readouts, replicates prior finding with new pathway\",\n      \"pmids\": [\"23275440\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"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.\",\n      \"method\": \"Co-immunoprecipitation; siRNA knockdown; ubiquitination assays; luciferase reporter assays; ChIP assay for p53 binding to S25 promoter; deletion/domain mapping mutants\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP, ubiquitination assay, ChIP, and domain mapping in single lab with multiple orthogonal methods\",\n      \"pmids\": [\"22777350\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"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.\",\n      \"method\": \"Expression of epitope-tagged RPS25 in Cos-1 cells; immunofluorescence; deletion mutagenesis; site-directed mutagenesis; chimeric construct analysis\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization with deletion and site-directed mutagenesis defining the targeting signal, functional consequence mapped\",\n      \"pmids\": [\"10050887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"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.\",\n      \"method\": \"Mutational analysis of yeast S25 NLS; nuclear/nucleolar localization assay in yeast\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — mutational analysis in yeast, single lab, single method described\",\n      \"pmids\": [\"10386617\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"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.\",\n      \"method\": \"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\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNA fractionation and protein-binding assays in single lab with multiple methods\",\n      \"pmids\": [\"11741912\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"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.\",\n      \"method\": \"Northern blot analysis; nuclear run-off transcription assay; cytoplasmic/nuclear/polysomal RNA fractionation; actinomycin D and cycloheximide treatment\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — nuclear run-off plus fractionation with multiple pharmacological controls, single lab\",\n      \"pmids\": [\"8144559\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"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.\",\n      \"method\": \"siRNA knockdown of RPS25 in mammalian cells; reporter assays for HIV-1 IRES activity; mutational analysis of HIV-1 5' leader structural domains\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA knockdown with reporter assays and mutational analysis of IRES, single lab\",\n      \"pmids\": [\"27191820\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"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.\",\n      \"method\": \"Genetic screen for regulators of RAN translation; validation in yeast, mammalian cells, and Drosophila models\",\n      \"journal\": \"Nature neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic screen plus multi-organism validation (yeast, mammalian, Drosophila), multiple orthogonal approaches\",\n      \"pmids\": [\"31358992\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"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.\",\n      \"method\": \"Kinetic binding studies (stopped-flow or equivalent); eS25 mutagenesis; 40S-IRES complex formation assays in vitro\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro kinetic reconstitution with mutagenesis defining mechanistic steps, single lab\",\n      \"pmids\": [\"32609821\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"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.\",\n      \"method\": \"CRISPR knockout of RPS25 in human cell lines; viral infection resistance assays; toxin resistance assays; cDNA rescue experiments; genomic locus repair; transcriptome analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple knockout clones, rescue experiments, genomic repair, transcriptomics, single lab\",\n      \"pmids\": [\"32463448\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"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.\",\n      \"method\": \"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\",\n      \"journal\": \"Leukemia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mRNA fractionation, protein expression, reporter assays, and functional readout, single lab with multiple methods\",\n      \"pmids\": [\"28260789\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1988,\n      \"finding\": \"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.\",\n      \"method\": \"Immobilized trypsin digestion of rat liver 40S subunits; protein identification by gel electrophoresis; electric birefringence to assess subunit conformation\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct biochemical localization with functional consequence (unfolding), single study\",\n      \"pmids\": [\"3378620\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"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.\",\n      \"method\": \"Comparative sequence alignment of bacterial and eukaryotic ribosomal proteins; analysis of rRNA contact residues from Thermus thermophilus 30S crystal structure\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Moderate — computational/comparative analysis, no direct experimental validation of rRNA contacts for eukaryotic S25\",\n      \"pmids\": [\"20034956\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"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.\",\n      \"method\": \"siRNA knockdown of eS25 in primary kidney cells; cell cycle analysis by flow cytometry; viral production assays for BKPyV\",\n      \"journal\": \"Philosophical transactions of the Royal Society of London. Series B, Biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — knockdown with cell cycle flow cytometry and viral production assay, single lab with two readouts\",\n      \"pmids\": [\"40045781\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"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.\",\n      \"method\": \"siRNA knockdown of RPS25 in mammalian cells; reporter assays for FMRpolyG RAN translation; toxicity assays\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA knockdown with functional RAN translation reporters, single lab, corroborates prior finding on RAN translation\",\n      \"pmids\": [\"40377206\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"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.\",\n      \"method\": \"RNAi knockdown of RpS25 in Drosophila testes; microscopic examination of spermatogenesis stages; actin cone and individualization complex assembly assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — tissue-specific knockdown in Drosophila with defined cellular phenotypes at multiple spermatogenesis stages, single lab\",\n      \"pmids\": [\"38341921\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RPS25 (eS25) is a surface-exposed protein of the 40S ribosomal subunit that directly contacts IRES RNA elements to mediate both initial binding and conformational stabilization of the 40S-IRES complex, making it specifically required for multiple non-canonical translation initiation mechanisms—including IRES-mediated initiation (CrPV IGR, HCV, HIV-1, poliovirus), ribosome shunting, and RAN translation—while being dispensable for cap-dependent translation; in addition, RPS25 interacts with MDM2 to inhibit its E3 ligase activity and stabilize p53 (forming a feedback loop where p53 represses RPS25 transcription), its mRNA undergoes stress-induced nuclear retention controlled by p53/MTF-1/La, and it plays roles in cell cycle progression and spermatogenesis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"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 [#1, #2]. 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 [#13]. 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 [#0, #1]; kinetic analysis shows it governs both the initial 40S-IRES binding step and the subsequent unimolecular conformational change that stabilizes the complex [#10]. 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 [#1, #2, #8]. 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 [#9, #16]. 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 [#3, #6, #7]. RPS25 also functions in cell cycle progression and in Drosophila spermatogenesis [#15, #17].\",\n  \"teleology\": [\n    {\n      \"year\": 1988,\n      \"claim\": \"Established the physical position of RPS25 on the ribosome, showing it is a surface-exposed 40S protein whose integrity stabilizes subunit conformation \\u2014 a structural prerequisite for later functional contacts.\",\n      \"evidence\": \"Immobilized trypsin digestion of rat liver 40S subunits with electric birefringence to assess conformation\",\n      \"pmids\": [\"3378620\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No atomic-resolution placement of RPS25 within the 40S\", \"Functional role beyond conformational stabilization not addressed\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"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.\",\n      \"evidence\": \"Northern blot, nuclear run-off, and nuclear/cytoplasmic/polysomal RNA fractionation under amino-acid deprivation in mammalian cells\",\n      \"pmids\": [\"8144559\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Trans-acting factors mediating nuclear retention not identified\", \"Physiological purpose of retention unresolved\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"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.\",\n      \"evidence\": \"Epitope-tagged deletion/site-directed mutants in Cos-1 cells with immunofluorescence; mutational NLS analysis in yeast\",\n      \"pmids\": [\"10050887\", \"10386617\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Import receptors not identified\", \"Relationship to ribosome assembly route not defined\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"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.\",\n      \"evidence\": \"Nuclear/cytoplasmic RNA fractionation and protein-interaction studies in hepatoma cells under nutrient deprivation\",\n      \"pmids\": [\"11741912\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct RNA-binding mechanism of each factor not fully resolved\", \"Generality beyond hepatoma cells untested\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"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.\",\n      \"evidence\": \"4-thiouridine crosslinking of the IGR-IRES to 40S proteins with site-directed IRES mutagenesis\",\n      \"pmids\": [\"17287295\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not test functional requirement of the contact\", \"Structural geometry of the interface unknown\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstrated RPS25 is specifically and functionally required for IRES-mediated initiation but dispensable for cap-dependent translation, using genetic deletion and in vitro reconstitution.\",\n      \"evidence\": \"Yeast deletion strains, in vitro 40S-IRES binding with purified Rps25-lacking 40S, and mammalian reporter assays\",\n      \"pmids\": [\"19952110\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"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)\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"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.\",\n      \"evidence\": \"siRNA knockdown with multi-virus amplification assays; Co-IP, ubiquitination, ChIP, and domain-mapping for the MDM2/p53 axis\",\n      \"pmids\": [\"23275440\", \"22777350\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether MDM2 binding is by free RPS25 or ribosome-bound RPS25 not resolved\", \"Structural basis of MDM2 inhibition unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"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.\",\n      \"evidence\": \"siRNA knockdown and HIV-1 IRES reporter assays with mutational dissection of the 5' leader\",\n      \"pmids\": [\"27191820\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct RPS25-HIV-1 IRES contact not mapped\", \"Mechanism of scanning-independent initiation not defined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Established RPS25 as a requirement for RAN translation of C9orf72 repeat expansions, connecting non-canonical initiation to neurodegenerative dipeptide-repeat toxicity.\",\n      \"evidence\": \"Genetic screen for RAN translation regulators validated in yeast, mammalian cells, and Drosophila\",\n      \"pmids\": [\"31358992\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether RPS25 contacts repeat RNA directly not shown\", \"Therapeutic tractability of targeting RPS25 unaddressed\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"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.\",\n      \"evidence\": \"Kinetic in vitro binding with eS25 mutagenesis; CRISPR knockout with cDNA rescue, genomic repair, and transcriptomics\",\n      \"pmids\": [\"32609821\", \"32463448\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of the non-rescuable cell-state transition unknown\", \"Structural model of the eS25 mutation effects on conformational change lacking\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Revealed translation-independent roles of RPS25 in cell cycle progression and additional RAN-translation substrates, expanding its functional repertoire beyond viral IRESes.\",\n      \"evidence\": \"siRNA knockdown with flow-cytometric cell cycle analysis and BKPyV assays; RAN translation reporters for FMR1 CGG repeats\",\n      \"pmids\": [\"40045781\", \"40377206\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism coupling RPS25 to cell cycle control unknown\", \"Whether cell-cycle role is ribosome-dependent unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"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.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No high-resolution structure of RPS25 engaging an IRES or repeat RNA\", \"Partition between ribosome-bound and free RPS25 pools across functions undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 10]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [13]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [1, 2, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4, 7]},\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [13, 1]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-72613\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [2, 8, 9]}\n    ],\n    \"complexes\": [\"40S ribosomal subunit\"],\n    \"partners\": [\"MDM2\", \"MDMX\", \"TP53\", \"MTF-1\", \"La (SSB)\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}