{"gene":"RPS27A","run_date":"2026-06-10T07:46:27","timeline":{"discoveries":[{"year":1989,"finding":"The longer C-terminal extension protein (CEP80) of the ubiquitin fusion gene is ribosomal protein S27a, localized to the 40S ribosomal subunit. Immunoblotting of rat 40S subunit proteins specifically identified CEP80 as ribosomal protein S27a.","method":"Immunoblotting of ribosomal subunit fractions; antibody-based identification","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct biochemical fractionation and immunoblotting, foundational finding replicated and built upon by many subsequent studies","pmids":["2538756"],"is_preprint":false},{"year":1995,"finding":"The rat ubiquitin-S27a fusion protein is processed in a reticulocyte lysate to release free ubiquitin and ribosomal protein S27a (80 amino acids). S27a contains a zinc finger motif of the C2-C2 variety.","method":"In vitro processing assay (reticulocyte lysate); recombinant cDNA characterization","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of proteolytic processing, directly demonstrated with recombinant proteins","pmids":["7488009"],"is_preprint":false},{"year":2000,"finding":"The human UBA80 (RPS27A) gene is located on chromosome 2p16, has a conserved 5'-end structure similar to UBA52 and other ribosomal gene promoters. Analysis identified a pseudogene for UBA80.","method":"Genomic mapping, promoter analysis, sequence comparison","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — genomic/structural characterization, single lab, sequence-based methods","pmids":["10772958"],"is_preprint":false},{"year":2011,"finding":"RPS27a interacts with MDM2 at its central acidic domain, suppresses MDM2-mediated p53 ubiquitination, leading to p53 activation and cell cycle arrest. Knockdown of S27a attenuates p53 activation in response to actinomycin D or 5-fluorouracil. MDM2 in turn ubiquitinates S27a and promotes its proteasomal degradation, forming a mutual regulatory loop.","method":"Co-immunoprecipitation, in vitro ubiquitination assay, shRNA knockdown, cell cycle analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP mapping to acidic domain, in vitro ubiquitination assay, and functional knockdown with defined phenotypic readout; multiple orthogonal methods in one study","pmids":["21561866"],"is_preprint":false},{"year":2011,"finding":"In the presence of HBx (hepatitis B virus), RPS27a shows a remarkable change in intracellular distribution: ubiquitin moiety shifts from cytoplasm to late-endosomal lysosomes, and the CEP (RPS27a) portion shifts from nucleoli to the perinucleolar region/nuclear foci. RPS27a accelerates cell cycle progression and cooperates with HBx.","method":"Immunofluorescence microscopy, RNA interference knockdown, cell cycle analysis","journal":"The Journal of general virology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct imaging of localization changes, RNAi functional validation; single lab, two methods","pmids":["22158882"],"is_preprint":false},{"year":2015,"finding":"The RPS27a gene is a direct transcriptional target of p53 and is overexpressed in response to DNA damage. Down-regulation of RPS27a by RNA interference blocked activation of p21(Waf1) in response to DNA damage, identifying RPS27a as a stress sensor that amplifies p53 response.","method":"Nuclear runoff/reporter assay, dominant-negative p53 mutant, RNA interference, Western blot","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct p53 transcriptional target assay with dominant-negative mutant, RNAi functional validation; single lab","pmids":["25592822"],"is_preprint":false},{"year":2017,"finding":"RPS27a interacts directly with EBV LMP1 in vitro and in vivo. Overexpression of RPS27a increases LMP1 half-life and completely inhibits LMP1 ubiquitination via the proteasome, stabilizing LMP1 and enhancing LMP1-mediated cell proliferation and invasion.","method":"Tandem affinity purification, co-immunoprecipitation, in vivo ubiquitination assay, shRNA knockdown, half-life analysis","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, in vivo ubiquitination assay, shRNA knockdown with functional readout; single lab","pmids":["28735865"],"is_preprint":false},{"year":2017,"finding":"Treatment with P-3F (a microtubule polymerization inhibitor) causes translocation of RPS27a from the nucleolus into the nucleoplasm, which decreases phosphorylation of MDM2 at serine 166 and inhibits MDM2-mediated ubiquitination of p53, resulting in p53 accumulation and cell cycle arrest at G2/M.","method":"Immunofluorescence (localization), Western blot (MDM2 phosphorylation, p53 levels), half-life assay","journal":"The international journal of biochemistry & cell biology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct imaging of nucleolar-to-nucleoplasm translocation with downstream signaling validation; single lab, two orthogonal methods","pmids":["28928040"],"is_preprint":false},{"year":2020,"finding":"USP16 is a deubiquitinase component of late cytoplasmic pre-40S subunits that removes ubiquitin from an internal lysine of RPS27a/eS31. USP16 deletion leads to late 40S subunit maturation defects, including incomplete 18S rRNA processing and retarded recycling of late-acting biogenesis factors. Ubiquitination of RPS27a depends on active translation.","method":"Mass spectrometry of pre-ribosomal subunits trapped on RIOK1, USP16 deletion/knockout, rRNA processing assay, CRISPR-based genetic analysis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — MS-based identification, genetic deletion with defined rRNA processing phenotype, mechanistic link between RPS27a ubiquitination and 40S maturation established with multiple methods","pmids":["32129764"],"is_preprint":false},{"year":2020,"finding":"DNA double-strand breaks (DSBs), including those induced by Cas9, trigger loss of RPS27a from ribosomes via p53-independent proteasomal degradation. Even a single DSB leads to altered translational output and ribosome remodeling, as shown by ribosome profiling.","method":"Ribosome profiling, mRNA-seq, proteasome inhibitor treatment, Cas9 vs dCas9 comparison, Western blot","journal":"The FEBS journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ribosome profiling plus proteasomal degradation assay, genetic controls (Cas9 vs dCas9); single lab, two orthogonal methods","pmids":["34914197"],"is_preprint":false},{"year":2022,"finding":"RPS27a directly binds RPL11 (confirmed by GST pull-down). Knockdown of RPS27a weakens the RPS27a-RPL11 interaction but enhances RPL11-MDM2 binding, thereby inhibiting MDM2-mediated ubiquitination and degradation of p53. RPS27a knockdown stabilizes p53 in an RPL11-dependent manner.","method":"Immunoprecipitation-proteomics, molecular docking, GST pull-down, Co-IP, in vitro ubiquitination assay, shRNA knockdown, xenograft model","journal":"Journal of experimental & clinical cancer research : CR","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — GST pull-down for direct binding, in vitro ubiquitination assay, in vivo xenograft validation, multiple orthogonal methods; single lab but comprehensive","pmids":["35073964"],"is_preprint":false},{"year":2022,"finding":"RPS27a is cleaved from the ubiquitin-RP precursor independently of ribosome biogenesis. In U2OS cells, knockdown of RPS27a does not stabilize p53 and does not block p53 stabilization following actinomycin D treatment. However, in MCF7 and LNCaP cells, knockdown of RPS27a robustly induces p53, consistent with other ribosomal proteins. RPS27a and RPL40 are needed for rRNA production in all cell lines tested.","method":"shRNA knockdown, Western blot, actinomycin D treatment, rRNA processing assay; multiple cell lines","journal":"Biomolecules","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic knockdown across cell lines with defined readouts; single lab, demonstrates cell-type specificity of p53 role","pmids":["37371478"],"is_preprint":false},{"year":2023,"finding":"UBA80 (RPS27A) interacts with H2A/H2AX histones and RNF168. Both UBA80 and UBA52 are recruited to laser-induced DNA damage sites. Ectopic expression of UBA80 inhibits RNF168-mediated H2A/H2AX ubiquitination at K13/15 and impairs 53BP1 recruitment to DNA lesions. The C-terminal ribosomal fragment (S27A) limits RNF168-nucleosome engagement by masking regulatory acidic residues E143/E144 and the nucleosome acidic patch.","method":"Co-immunoprecipitation, laser micro-irradiation live-cell imaging, domain mapping, H2A ubiquitination assay, 53BP1 foci assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, live-cell DNA damage recruitment assay, domain-level mechanistic dissection, functional ubiquitination and 53BP1 readouts; multiple orthogonal methods","pmids":["37451480"],"is_preprint":false},{"year":2021,"finding":"PICT1 regulates the Rps27a-Mdm2-p53 pathway: reduction of PICT1 levels by P-3F (via decreased STMN1 serine 16 phosphorylation) leads to translocation of Rps27a from the nucleolus to the nucleoplasm, where it inhibits Mdm2-mediated p53 ubiquitination, enhancing p53 stability.","method":"Immunofluorescence, Co-IP, Western blot, siRNA knockdown of PICT1","journal":"Biochimica et biophysica acta. Molecular cell research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct imaging of RPS27a relocalization, PICT1 knockdown with pathway readout; single lab","pmids":["34166715"],"is_preprint":false},{"year":2016,"finding":"Phospho-STAT3 transactivates RPS27a through specific binding sites in the RPS27a gene promoter (at positions -633 to -625 and -486 to -478), in a dose-dependent manner, linking BCR-ABL/STAT3 signaling to RPS27a expression in CML cells.","method":"Chromatin immunoprecipitation (ChIP), promoter reporter assay, STAT3 inhibitor (WP1066), Western blot","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and promoter reporter assay identify specific binding sites; single lab, two orthogonal methods","pmids":["26942564"],"is_preprint":false},{"year":2024,"finding":"TRIM13 interacts with RPS27A and acts as an E3 ubiquitin ligase that ubiquitinates RPS27A, promoting its degradation. TRIM13-mediated RPS27A degradation inhibits NF-κB signaling and suppresses lung cancer progression. RPS27A overexpression reverses the inhibitory effect of TRIM13 on NF-κB signaling.","method":"Co-immunoprecipitation, ubiquitination assay, overexpression/knockdown, NF-κB reporter, in vitro and in vivo tumor models","journal":"Physiological reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus ubiquitination assay with functional rescue; single lab, two orthogonal methods","pmids":["39667820"],"is_preprint":false},{"year":2024,"finding":"RPS27A interacts with PSMD12 and regulates the PSMD12/NF-κB signaling axis in microglia. Silencing RPS27A in OGD/R-induced microglia decreases inflammatory factor release and reduces neuron apoptosis, and in vivo silencing of RPS27A reduces neutrophil infiltration and improves outcomes in cerebral ischemia-reperfusion injury.","method":"siRNA knockdown, OGD/R model, MCAO model, cytokine assays, Western blot","journal":"Molecular medicine (Cambridge, Mass.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro and in vivo loss-of-function with defined pathway readout; single lab, two model systems","pmids":["39069432"],"is_preprint":false},{"year":2024,"finding":"ASFV protein pCP312R interacts with RPS27A (a component of the 40S ribosomal subunit), causing modification in the subcellular localization of RPS27A, which suppresses host protein translation. Knockout of RPS27A completely abolished the host protein shutoff activity of pCP312R.","method":"LC-MS/co-immunoprecipitation, crystal structure of pCP312R, confocal microscopy, Renilla-Glo luciferase assay, ribopuromycylation, RPS27A knockout/complementation","journal":"International journal of biological macromolecules","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — crystal structure of viral binding partner, Co-IP, genetic knockout with functional complementation, and multiple translation assays; multiple orthogonal methods","pmids":["39069039"],"is_preprint":false},{"year":2005,"finding":"Ubiquitin/ribosomal protein S27a was identified as an interacting protein of protein kinase CK2alpha' subunit by yeast two-hybrid screening of an HL-60 cell cDNA library.","method":"Yeast two-hybrid screening","journal":"Ai zheng = Aizheng = Chinese journal of cancer","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single yeast two-hybrid result, no validation by orthogonal method","pmids":["15642198"],"is_preprint":false},{"year":2009,"finding":"Structural analysis identified that the conserved structural motifs of bacterial ribosomal protein S16p that contact rRNA in the 30S subunit are present in eukaryotic ribosomal protein S27Ae (RPS27A), suggesting these families are homologous.","method":"Sequence alignment and comparative structural analysis with T. thermophilus 30S crystal structure","journal":"Nucleic acids research","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational sequence/structural comparison, no direct experimental validation of rRNA contact for RPS27A","pmids":["20034956"],"is_preprint":false},{"year":2025,"finding":"HucMSC-derived extracellular vesicles deliver RPS27A protein to neurons. RPS27A binds to the MDM2 promoter, promoting p53 ubiquitination and degradation, thereby exerting neuroprotective effects in Parkinson's disease models. MDM2 overexpression strengthened the therapeutic effect.","method":"EV co-culture, RPS27A silencing, chromatin immunoprecipitation (ChIP) for MDM2 promoter binding, MDM2 overexpression rescue, in vitro and in vivo PD models","journal":"Journal of neuroimmune pharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP demonstrating RPS27A binding to MDM2 promoter, functional rescue with MDM2 overexpression; single lab","pmids":["40338442"],"is_preprint":false}],"current_model":"RPS27A is a small 40S ribosomal subunit protein synthesized as a ubiquitin fusion precursor (Ub-RPS27a) that is co-translationally cleaved by deubiquitinases (including USP16, which also removes ubiquitin from an internal lysine of RPS27a to promote late 40S maturation); beyond its ribosomal role, RPS27A functions as an extraribosomal regulator of the MDM2-p53 axis by binding the MDM2 acidic domain to suppress MDM2-mediated p53 ubiquitination, while MDM2 reciprocally ubiquitinates RPS27A for proteasomal degradation; RPS27A also directly binds RPL11 to modulate RPL11-MDM2 interaction during ribosomal stress, undergoes nucleolar-to-nucleoplasm translocation to regulate p53 stability, antagonizes RNF168-mediated histone H2A ubiquitination at DNA damage sites through its C-terminal domain, is transcriptionally activated by p53 (forming a feedback loop) and by phospho-STAT3, and is ubiquitinated and degraded by the E3 ligase TRIM13 to suppress NF-κB signaling."},"narrative":{"mechanistic_narrative":"RPS27A is a structural protein of the small (40S) ribosomal subunit that is synthesized as a ubiquitin fusion precursor (Ub-RPS27a) and processed to release free ubiquitin and the 80-residue C2-C2 zinc-finger ribosomal protein [PMID:2538756, PMID:7488009]. During late cytoplasmic 40S maturation the deubiquitinase USP16 removes ubiquitin from an internal lysine of RPS27a/eS31 in a translation-dependent manner, and loss of USP16 causes 18S rRNA processing defects and impaired recycling of biogenesis factors [PMID:32129764]; RPS27A itself is required for rRNA production across cell lines [PMID:37371478]. Beyond the ribosome, RPS27A is an extraribosomal regulator of the MDM2–p53 axis: it binds the MDM2 central acidic domain to suppress MDM2-mediated p53 ubiquitination and drive p53 activation and cell-cycle arrest, while MDM2 reciprocally ubiquitinates RPS27A for proteasomal degradation [PMID:21561866], and it directly binds RPL11 to tune the RPL11–MDM2 interaction during ribosomal stress [PMID:35073964]. This regulation is coupled to nucleolar-to-nucleoplasm translocation of RPS27A that lowers MDM2 Ser166 phosphorylation and stabilizes p53 [PMID:28928040, PMID:34166715], and RPS27A is itself a direct p53 transcriptional target that amplifies the damage response [PMID:25592822]. In the DNA-damage response RPS27A is recruited to lesions and, through its C-terminal ribosomal fragment, antagonizes RNF168-mediated H2A/H2AX K13/15 ubiquitination by masking the nucleosome acidic patch, impairing 53BP1 recruitment [PMID:37451480]. RPS27A also controls NF-κB signaling, being targeted for degradation by the E3 ligase TRIM13 [PMID:39667820] and acting through a PSMD12/NF-κB axis in microglia [PMID:39069432]. RPS27A is exploited by multiple pathogens, whose proteins bind it to stabilize viral oncoproteins or to shut off host translation [PMID:28735865, PMID:39069039].","teleology":[{"year":1989,"claim":"Established that the longer C-terminal extension of the ubiquitin fusion gene is a bona fide ribosomal protein, defining RPS27A's core identity as a 40S subunit component.","evidence":"Immunoblotting of rat 40S subunit protein fractions","pmids":["2538756"],"confidence":"High","gaps":["Did not establish rRNA contacts or assembly role","Functional consequence of ribosomal incorporation not addressed"]},{"year":1995,"claim":"Showed that the ubiquitin-S27a precursor is proteolytically processed to free ubiquitin plus an 80-aa zinc-finger protein, defining the precursor maturation step and RPS27A domain architecture.","evidence":"In vitro processing in reticulocyte lysate; recombinant cDNA characterization","pmids":["7488009"],"confidence":"High","gaps":["Protease responsible not identified","Functional role of the C2-C2 zinc finger unresolved"]},{"year":2005,"claim":"First proposed a non-ribosomal partner by identifying RPS27A as a CK2alpha' interactor, raising the possibility of signaling roles.","evidence":"Yeast two-hybrid screen of HL-60 cDNA library","pmids":["15642198"],"confidence":"Low","gaps":["Single Y2H hit with no orthogonal validation","No functional consequence demonstrated"]},{"year":2011,"claim":"Defined RPS27A as an extraribosomal regulator of p53 by mapping its binding to the MDM2 acidic domain and demonstrating a reciprocal MDM2-RPS27A regulatory loop.","evidence":"Co-IP, in vitro ubiquitination, shRNA knockdown, cell-cycle analysis under ribosomal stress","pmids":["21561866","22158882"],"confidence":"High","gaps":["Structural basis of the acidic-domain interaction not resolved","Trigger for the nucleolar release of RPS27A not defined"]},{"year":2015,"claim":"Placed RPS27A within a p53 feedback loop by showing it is a direct p53 transcriptional target required to amplify the p21 damage response.","evidence":"Reporter/runoff assay with dominant-negative p53 and RNAi, Western blot","pmids":["25592822"],"confidence":"Medium","gaps":["p53 response element not finely mapped","Cell-type generality not tested"]},{"year":2016,"claim":"Linked oncogenic signaling to RPS27A expression by demonstrating phospho-STAT3 transactivation through defined promoter elements.","evidence":"ChIP, promoter reporter, STAT3 inhibitor, Western blot in CML cells","pmids":["26942564"],"confidence":"Medium","gaps":["Downstream consequence of elevated RPS27A in CML not mechanistically dissected","Single cell context"]},{"year":2017,"claim":"Connected drug-induced microtubule perturbation to p53 activation through nucleolar-to-nucleoplasm translocation of RPS27A and reduced MDM2 Ser166 phosphorylation.","evidence":"Immunofluorescence localization, Western blot, half-life assays; viral oncoprotein stabilization assays","pmids":["28928040","28735865"],"confidence":"Medium","gaps":["Molecular driver of translocation incompletely defined","How RPS27A alters MDM2 phosphorylation not established"]},{"year":2020,"claim":"Established the deubiquitination step in 40S maturation (USP16 removing ubiquitin from RPS27a) and showed DNA breaks deplete RPS27a from ribosomes to remodel translation.","evidence":"MS of trapped pre-40S, USP16 deletion with rRNA processing assay; ribosome profiling with Cas9/dCas9 controls and proteasome inhibition","pmids":["32129764","34914197"],"confidence":"High","gaps":["E3 ligase adding the internal ubiquitin not identified","Translational targets remodeled after RPS27a loss not fully cataloged"]},{"year":2022,"claim":"Refined the p53 mechanism by identifying direct RPS27A-RPL11 binding that gates RPL11-MDM2 interaction, and revealed cell-type-dependent p53 dependence on RPS27A.","evidence":"GST pull-down, Co-IP, in vitro ubiquitination, xenograft; systematic knockdown across multiple cell lines","pmids":["35073964","37371478"],"confidence":"High","gaps":["Basis for cell-type variability in p53 response unexplained","Stoichiometry of the RPS27A-RPL11-MDM2 assembly unknown"]},{"year":2023,"claim":"Defined a chromatin-level function in which the RPS27A C-terminal fragment masks the nucleosome acidic patch to antagonize RNF168 H2A ubiquitination and 53BP1 recruitment.","evidence":"Co-IP, laser micro-irradiation imaging, domain mapping, H2A ubiquitination and 53BP1 foci assays","pmids":["37451480"],"confidence":"High","gaps":["Regulation of RPS27A recruitment to damage sites not defined","Relationship between this role and its ribosomal pool unclear"]},{"year":2024,"claim":"Connected RPS27A to NF-κB control through TRIM13-mediated degradation and a PSMD12/NF-κB axis, and demonstrated pathogen hijacking for host translational shutoff.","evidence":"Co-IP and ubiquitination assays with NF-κB reporters and tumor models; ASFV pCP312R crystal structure, Co-IP, RPS27A knockout/complementation, translation assays","pmids":["39667820","39069432","39069039"],"confidence":"Medium","gaps":["Direct mechanism by which RPS27A modulates NF-κB not resolved","Whether translational and signaling pools are distinct unclear"]},{"year":2025,"claim":"Showed RPS27A can act in trans, delivered by extracellular vesicles, binding the MDM2 promoter to promote p53 degradation and confer neuroprotection.","evidence":"EV co-culture, ChIP for MDM2 promoter binding, MDM2-overexpression rescue, PD models","pmids":["40338442"],"confidence":"Medium","gaps":["Direct DNA-binding activity of RPS27A at the MDM2 promoter not biochemically characterized","Reconciliation with RPS27A's p53-stabilizing roles in other contexts unaddressed"]},{"year":null,"claim":"How RPS27A partitions between its ribosomal, p53-regulatory, chromatin, and NF-κB functions, and what governs its release from the nucleolus and ribosome, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model linking ribosomal incorporation to extraribosomal pools","Signals controlling subcellular redistribution not defined","Structural basis of MDM2/RPL11/nucleosome interactions incomplete"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,10,12]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[20]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[0,17]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[4,7,13]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[7,13]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[12,20]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[8,11]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[9,12]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[3,5]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[15,16]}],"complexes":["40S ribosomal subunit"],"partners":["MDM2","RPL11","USP16","RNF168","TRIM13","PSMD12","STAT3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P62979","full_name":"Ubiquitin-ribosomal protein eS31 fusion protein","aliases":["Ubiquitin carboxyl extension protein 80"],"length_aa":156,"mass_kda":18.0,"function":"Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in proteotoxic stress response and cell cycle; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling Component of the 40S subunit of the ribosome (PubMed:23636399, PubMed:9582194). Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome (PubMed:23636399, PubMed:34516797)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/P62979/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPS27A","classification":"Common Essential","n_dependent_lines":1206,"n_total_lines":1208,"dependency_fraction":0.9983443708609272},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PSMB1","stoichiometry":10.0},{"gene":"PTMA","stoichiometry":10.0},{"gene":"UBA52","stoichiometry":10.0},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"CLTA","stoichiometry":0.2},{"gene":"COPA","stoichiometry":0.2},{"gene":"COPE","stoichiometry":0.2},{"gene":"HIST2H2BE","stoichiometry":0.2},{"gene":"HMGN5","stoichiometry":0.2},{"gene":"PARP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RPS27A","total_profiled":1310},"omim":[{"mim_id":"191343","title":"RIBOSOMAL PROTEIN S27a; RPS27A","url":"https://www.omim.org/entry/191343"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoli","reliability":"Supported"},{"location":"Endoplasmic reticulum","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"},{"location":"Acrosome","reliability":"Additional"},{"location":"Equatorial segment","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPS27A"},"hgnc":{"alias_symbol":["UBCEP80","Uba80","S27A","eS31"],"prev_symbol":[]},"alphafold":{"accession":"P62979","domains":[{"cath_id":"3.10.20.90","chopping":"1-70","consensus_level":"high","plddt":92.6919,"start":1,"end":70},{"cath_id":"-","chopping":"113-156","consensus_level":"medium","plddt":87.8139,"start":113,"end":156}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P62979","model_url":"https://alphafold.ebi.ac.uk/files/AF-P62979-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P62979-F1-predicted_aligned_error_v6.png","plddt_mean":89.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPS27A","jax_strain_url":"https://www.jax.org/strain/search?query=RPS27A"},"sequence":{"accession":"P62979","fasta_url":"https://rest.uniprot.org/uniprotkb/P62979.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P62979/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P62979"}},"corpus_meta":[{"pmid":"2538756","id":"PMC_2538756","title":"Identification of the long ubiquitin extension as ribosomal protein S27a.","date":"1989","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/2538756","citation_count":215,"is_preprint":false},{"pmid":"21561866","id":"PMC_21561866","title":"Interplay between ribosomal protein S27a and MDM2 protein in p53 activation in response to ribosomal stress.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21561866","citation_count":87,"is_preprint":false},{"pmid":"35073964","id":"PMC_35073964","title":"Loss of RPS27a expression regulates the cell cycle, apoptosis, and proliferation via the RPL11-MDM2-p53 pathway in lung adenocarcinoma cells.","date":"2022","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/35073964","citation_count":71,"is_preprint":false},{"pmid":"8385574","id":"PMC_8385574","title":"Ubiquitin-ribosomal protein S27a gene overexpressed in human colorectal carcinoma is an early growth response gene.","date":"1993","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/8385574","citation_count":69,"is_preprint":false},{"pmid":"24680683","id":"PMC_24680683","title":"RPS27a promotes proliferation, regulates cell cycle progression and inhibits apoptosis of leukemia cells.","date":"2014","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/24680683","citation_count":55,"is_preprint":false},{"pmid":"7488009","id":"PMC_7488009","title":"The carboxyl extensions of two rat ubiquitin fusion proteins are ribosomal proteins S27a and L40.","date":"1995","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/7488009","citation_count":42,"is_preprint":false},{"pmid":"36580426","id":"PMC_36580426","title":"Multifaceted functions of RPS27a: An unconventional ribosomal protein.","date":"2022","source":"Journal of cellular 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induces the expression of ribosomal protein S27a gene in a p53-dependent manner.","date":"2015","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/25592822","citation_count":31,"is_preprint":false},{"pmid":"10772958","id":"PMC_10772958","title":"Structure of the human ubiquitin fusion gene Uba80 (RPS27a) and one of its pseudogenes.","date":"2000","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/10772958","citation_count":28,"is_preprint":false},{"pmid":"22158882","id":"PMC_22158882","title":"The HBx protein of hepatitis B virus regulates the expression, intracellular distribution and functions of ribosomal protein S27a.","date":"2011","source":"The Journal of general virology","url":"https://pubmed.ncbi.nlm.nih.gov/22158882","citation_count":27,"is_preprint":false},{"pmid":"28735865","id":"PMC_28735865","title":"RPS27a enhances EBV-encoded LMP1-mediated proliferation and invasion by stabilizing of LMP1.","date":"2017","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/28735865","citation_count":26,"is_preprint":false},{"pmid":"34914197","id":"PMC_34914197","title":"Double stranded DNA breaks and genome editing trigger loss of ribosomal protein RPS27A.","date":"2022","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/34914197","citation_count":24,"is_preprint":false},{"pmid":"26942564","id":"PMC_26942564","title":"Overexpression of RPS27a contributes to enhanced chemoresistance of CML cells to imatinib by the transactivated STAT3.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/26942564","citation_count":22,"is_preprint":false},{"pmid":"30272249","id":"PMC_30272249","title":"Nicotine Promotes Human Papillomavirus (HPV)-Immortalized Cervical Epithelial Cells (H8) Proliferation by Activating RPS27a-Mdm2-P53 Pathway In Vitro.","date":"2019","source":"Toxicological sciences : an official journal of the Society of Toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/30272249","citation_count":20,"is_preprint":false},{"pmid":"39994725","id":"PMC_39994725","title":"CircAKT3 promotes prostate cancer proliferation and metastasis by enhancing the binding of RPS27A and RPL11.","date":"2025","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/39994725","citation_count":16,"is_preprint":false},{"pmid":"33564284","id":"PMC_33564284","title":"Apolipoprotein M promotes growth and inhibits apoptosis of colorectal cancer cells through upregulation of ribosomal protein S27a.","date":"2021","source":"EXCLI journal","url":"https://pubmed.ncbi.nlm.nih.gov/33564284","citation_count":15,"is_preprint":false},{"pmid":"19479258","id":"PMC_19479258","title":"The ubiquitin extension protein S27a is differentially expressed in developing flower organs of Thompson seedless versus Thompson seeded grape isogenic clones.","date":"2009","source":"Plant cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/19479258","citation_count":15,"is_preprint":false},{"pmid":"24833360","id":"PMC_24833360","title":"Inverse correlation of ribosomal protein S27A and multifunctional protein YB-1 in hepatocellular carcinoma.","date":"2014","source":"Clinical biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24833360","citation_count":12,"is_preprint":false},{"pmid":"34166715","id":"PMC_34166715","title":"PICT1 is critical for regulating the Rps27a-Mdm2-p53 pathway by microtubule polymerization inhibitor against cervical cancer.","date":"2021","source":"Biochimica et biophysica acta. Molecular cell research","url":"https://pubmed.ncbi.nlm.nih.gov/34166715","citation_count":12,"is_preprint":false},{"pmid":"28928040","id":"PMC_28928040","title":"P-3F, a microtubule polymerization inhibitor enhances P53 stability through the change in localization of RPS27a.","date":"2017","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/28928040","citation_count":11,"is_preprint":false},{"pmid":"37371478","id":"PMC_37371478","title":"RPS27a and RPL40, Which Are Produced as Ubiquitin Fusion Proteins, Are Not Essential for p53 Signalling.","date":"2023","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/37371478","citation_count":10,"is_preprint":false},{"pmid":"39039432","id":"PMC_39039432","title":"Modulating the RPS27A/PSMD12/NF-κB pathway to control immune response in mouse brain ischemia-reperfusion injury.","date":"2024","source":"Molecular medicine (Cambridge, Mass.)","url":"https://pubmed.ncbi.nlm.nih.gov/39039432","citation_count":10,"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":"26493147","id":"PMC_26493147","title":"Suppression and overexpression of ubiquitin extension protein S27a affects cell proliferation and in vitro regeneration in Nicotiana benthamiana.","date":"2009","source":"Plant science : an international journal of experimental plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/26493147","citation_count":8,"is_preprint":false},{"pmid":"37451480","id":"PMC_37451480","title":"UBA80 and UBA52 fine-tune RNF168-dependent histone ubiquitination and DNA repair.","date":"2023","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37451480","citation_count":7,"is_preprint":false},{"pmid":"39069039","id":"PMC_39069039","title":"African swine fever virus pCP312R interacts with host RPS27A to shut off host protein translation and promotes viral replication.","date":"2024","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/39069039","citation_count":7,"is_preprint":false},{"pmid":"37667747","id":"PMC_37667747","title":"Chidamide and Oxaliplatin Synergistically Inhibit Colorectal Cancer Growth by Regulating the RPS27A-MDM2-P53 Axis.","date":"2023","source":"OncoTargets and therapy","url":"https://pubmed.ncbi.nlm.nih.gov/37667747","citation_count":6,"is_preprint":false},{"pmid":"28913776","id":"PMC_28913776","title":"Interactions of antisera to different Chlamydia and Chlamydophila species with the ribosomal protein RPS27a correlate with impaired protein synthesis in a human choroid plexus papilloma cell line.","date":"2017","source":"Immunologic research","url":"https://pubmed.ncbi.nlm.nih.gov/28913776","citation_count":6,"is_preprint":false},{"pmid":"40338442","id":"PMC_40338442","title":"HucMSCs-Derived Extracellular Vesicles Deliver RPS27A Protein to Manipulate the MDM2-P53 Axis and Ameliorate Neurological Dysfunction in Parkinson's Disease.","date":"2025","source":"Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/40338442","citation_count":1,"is_preprint":false},{"pmid":"39667820","id":"PMC_39667820","title":"Trim13-induced ubiquitination of RPS27A inhibits the progression of lung cancer by depending on the inactivation of NF-κB signaling pathway.","date":"2024","source":"Physiological reports","url":"https://pubmed.ncbi.nlm.nih.gov/39667820","citation_count":1,"is_preprint":false},{"pmid":"18257223","id":"PMC_18257223","title":"[The connection between tumor and ubiquitin-ribosomal protein S27a, ubiquitin and ribosomal protein].","date":"2007","source":"Sheng wu gong cheng xue bao = Chinese journal of biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/18257223","citation_count":0,"is_preprint":false},{"pmid":"42082087","id":"PMC_42082087","title":"Identification and characterization of 40S ribosomal protein S27a as an antimicrobial protein from starfish, Patiria pectinifera.","date":"2026","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/42082087","citation_count":0,"is_preprint":false},{"pmid":"41902225","id":"PMC_41902225","title":"The Avian Influenza Virus PA Protein Recruits Host RPS27A to Support Viral Replication.","date":"2026","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/41902225","citation_count":0,"is_preprint":false},{"pmid":"15642198","id":"PMC_15642198","title":"[Screening ubiquitin/ribosomal protein S27a by yeast two-hybridization system].","date":"2005","source":"Ai zheng = Aizheng = Chinese journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/15642198","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.07.30.605947","title":"IDENTIFICATION OF IMMUNE RESPONSE AND RNA NETWORK OF RHEUMATOID ARTHRITIS AND MOLECULAR DOCKING OF  <i>CELASTRUS PANICULATUS</i>  AS POTENTIAL THERAPEUTIC AGENT","date":"2024-08-01","source":"bioRxiv","url":"https://doi.org/10.1101/2024.07.30.605947","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":20452,"output_tokens":5200,"usd":0.069678,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13460,"output_tokens":4087,"usd":0.084737,"stage2_stop_reason":"end_turn"},"total_usd":0.154415,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1989,\n      \"finding\": \"The longer C-terminal extension protein (CEP80) of the ubiquitin fusion gene is ribosomal protein S27a, localized to the 40S ribosomal subunit. Immunoblotting of rat 40S subunit proteins specifically identified CEP80 as ribosomal protein S27a.\",\n      \"method\": \"Immunoblotting of ribosomal subunit fractions; antibody-based identification\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct biochemical fractionation and immunoblotting, foundational finding replicated and built upon by many subsequent studies\",\n      \"pmids\": [\"2538756\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"The rat ubiquitin-S27a fusion protein is processed in a reticulocyte lysate to release free ubiquitin and ribosomal protein S27a (80 amino acids). S27a contains a zinc finger motif of the C2-C2 variety.\",\n      \"method\": \"In vitro processing assay (reticulocyte lysate); recombinant cDNA characterization\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of proteolytic processing, directly demonstrated with recombinant proteins\",\n      \"pmids\": [\"7488009\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"The human UBA80 (RPS27A) gene is located on chromosome 2p16, has a conserved 5'-end structure similar to UBA52 and other ribosomal gene promoters. Analysis identified a pseudogene for UBA80.\",\n      \"method\": \"Genomic mapping, promoter analysis, sequence comparison\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — genomic/structural characterization, single lab, sequence-based methods\",\n      \"pmids\": [\"10772958\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"RPS27a interacts with MDM2 at its central acidic domain, suppresses MDM2-mediated p53 ubiquitination, leading to p53 activation and cell cycle arrest. Knockdown of S27a attenuates p53 activation in response to actinomycin D or 5-fluorouracil. MDM2 in turn ubiquitinates S27a and promotes its proteasomal degradation, forming a mutual regulatory loop.\",\n      \"method\": \"Co-immunoprecipitation, in vitro ubiquitination assay, shRNA knockdown, cell cycle analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP mapping to acidic domain, in vitro ubiquitination assay, and functional knockdown with defined phenotypic readout; multiple orthogonal methods in one study\",\n      \"pmids\": [\"21561866\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"In the presence of HBx (hepatitis B virus), RPS27a shows a remarkable change in intracellular distribution: ubiquitin moiety shifts from cytoplasm to late-endosomal lysosomes, and the CEP (RPS27a) portion shifts from nucleoli to the perinucleolar region/nuclear foci. RPS27a accelerates cell cycle progression and cooperates with HBx.\",\n      \"method\": \"Immunofluorescence microscopy, RNA interference knockdown, cell cycle analysis\",\n      \"journal\": \"The Journal of general virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct imaging of localization changes, RNAi functional validation; single lab, two methods\",\n      \"pmids\": [\"22158882\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The RPS27a gene is a direct transcriptional target of p53 and is overexpressed in response to DNA damage. Down-regulation of RPS27a by RNA interference blocked activation of p21(Waf1) in response to DNA damage, identifying RPS27a as a stress sensor that amplifies p53 response.\",\n      \"method\": \"Nuclear runoff/reporter assay, dominant-negative p53 mutant, RNA interference, Western blot\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct p53 transcriptional target assay with dominant-negative mutant, RNAi functional validation; single lab\",\n      \"pmids\": [\"25592822\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"RPS27a interacts directly with EBV LMP1 in vitro and in vivo. Overexpression of RPS27a increases LMP1 half-life and completely inhibits LMP1 ubiquitination via the proteasome, stabilizing LMP1 and enhancing LMP1-mediated cell proliferation and invasion.\",\n      \"method\": \"Tandem affinity purification, co-immunoprecipitation, in vivo ubiquitination assay, shRNA knockdown, half-life analysis\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, in vivo ubiquitination assay, shRNA knockdown with functional readout; single lab\",\n      \"pmids\": [\"28735865\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Treatment with P-3F (a microtubule polymerization inhibitor) causes translocation of RPS27a from the nucleolus into the nucleoplasm, which decreases phosphorylation of MDM2 at serine 166 and inhibits MDM2-mediated ubiquitination of p53, resulting in p53 accumulation and cell cycle arrest at G2/M.\",\n      \"method\": \"Immunofluorescence (localization), Western blot (MDM2 phosphorylation, p53 levels), half-life assay\",\n      \"journal\": \"The international journal of biochemistry & cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct imaging of nucleolar-to-nucleoplasm translocation with downstream signaling validation; single lab, two orthogonal methods\",\n      \"pmids\": [\"28928040\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"USP16 is a deubiquitinase component of late cytoplasmic pre-40S subunits that removes ubiquitin from an internal lysine of RPS27a/eS31. USP16 deletion leads to late 40S subunit maturation defects, including incomplete 18S rRNA processing and retarded recycling of late-acting biogenesis factors. Ubiquitination of RPS27a depends on active translation.\",\n      \"method\": \"Mass spectrometry of pre-ribosomal subunits trapped on RIOK1, USP16 deletion/knockout, rRNA processing assay, CRISPR-based genetic analysis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — MS-based identification, genetic deletion with defined rRNA processing phenotype, mechanistic link between RPS27a ubiquitination and 40S maturation established with multiple methods\",\n      \"pmids\": [\"32129764\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"DNA double-strand breaks (DSBs), including those induced by Cas9, trigger loss of RPS27a from ribosomes via p53-independent proteasomal degradation. Even a single DSB leads to altered translational output and ribosome remodeling, as shown by ribosome profiling.\",\n      \"method\": \"Ribosome profiling, mRNA-seq, proteasome inhibitor treatment, Cas9 vs dCas9 comparison, Western blot\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ribosome profiling plus proteasomal degradation assay, genetic controls (Cas9 vs dCas9); single lab, two orthogonal methods\",\n      \"pmids\": [\"34914197\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RPS27a directly binds RPL11 (confirmed by GST pull-down). Knockdown of RPS27a weakens the RPS27a-RPL11 interaction but enhances RPL11-MDM2 binding, thereby inhibiting MDM2-mediated ubiquitination and degradation of p53. RPS27a knockdown stabilizes p53 in an RPL11-dependent manner.\",\n      \"method\": \"Immunoprecipitation-proteomics, molecular docking, GST pull-down, Co-IP, in vitro ubiquitination assay, shRNA knockdown, xenograft model\",\n      \"journal\": \"Journal of experimental & clinical cancer research : CR\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — GST pull-down for direct binding, in vitro ubiquitination assay, in vivo xenograft validation, multiple orthogonal methods; single lab but comprehensive\",\n      \"pmids\": [\"35073964\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RPS27a is cleaved from the ubiquitin-RP precursor independently of ribosome biogenesis. In U2OS cells, knockdown of RPS27a does not stabilize p53 and does not block p53 stabilization following actinomycin D treatment. However, in MCF7 and LNCaP cells, knockdown of RPS27a robustly induces p53, consistent with other ribosomal proteins. RPS27a and RPL40 are needed for rRNA production in all cell lines tested.\",\n      \"method\": \"shRNA knockdown, Western blot, actinomycin D treatment, rRNA processing assay; multiple cell lines\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic knockdown across cell lines with defined readouts; single lab, demonstrates cell-type specificity of p53 role\",\n      \"pmids\": [\"37371478\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"UBA80 (RPS27A) interacts with H2A/H2AX histones and RNF168. Both UBA80 and UBA52 are recruited to laser-induced DNA damage sites. Ectopic expression of UBA80 inhibits RNF168-mediated H2A/H2AX ubiquitination at K13/15 and impairs 53BP1 recruitment to DNA lesions. The C-terminal ribosomal fragment (S27A) limits RNF168-nucleosome engagement by masking regulatory acidic residues E143/E144 and the nucleosome acidic patch.\",\n      \"method\": \"Co-immunoprecipitation, laser micro-irradiation live-cell imaging, domain mapping, H2A ubiquitination assay, 53BP1 foci assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, live-cell DNA damage recruitment assay, domain-level mechanistic dissection, functional ubiquitination and 53BP1 readouts; multiple orthogonal methods\",\n      \"pmids\": [\"37451480\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"PICT1 regulates the Rps27a-Mdm2-p53 pathway: reduction of PICT1 levels by P-3F (via decreased STMN1 serine 16 phosphorylation) leads to translocation of Rps27a from the nucleolus to the nucleoplasm, where it inhibits Mdm2-mediated p53 ubiquitination, enhancing p53 stability.\",\n      \"method\": \"Immunofluorescence, Co-IP, Western blot, siRNA knockdown of PICT1\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct imaging of RPS27a relocalization, PICT1 knockdown with pathway readout; single lab\",\n      \"pmids\": [\"34166715\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Phospho-STAT3 transactivates RPS27a through specific binding sites in the RPS27a gene promoter (at positions -633 to -625 and -486 to -478), in a dose-dependent manner, linking BCR-ABL/STAT3 signaling to RPS27a expression in CML cells.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), promoter reporter assay, STAT3 inhibitor (WP1066), Western blot\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and promoter reporter assay identify specific binding sites; single lab, two orthogonal methods\",\n      \"pmids\": [\"26942564\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM13 interacts with RPS27A and acts as an E3 ubiquitin ligase that ubiquitinates RPS27A, promoting its degradation. TRIM13-mediated RPS27A degradation inhibits NF-κB signaling and suppresses lung cancer progression. RPS27A overexpression reverses the inhibitory effect of TRIM13 on NF-κB signaling.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, overexpression/knockdown, NF-κB reporter, in vitro and in vivo tumor models\",\n      \"journal\": \"Physiological reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus ubiquitination assay with functional rescue; single lab, two orthogonal methods\",\n      \"pmids\": [\"39667820\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RPS27A interacts with PSMD12 and regulates the PSMD12/NF-κB signaling axis in microglia. Silencing RPS27A in OGD/R-induced microglia decreases inflammatory factor release and reduces neuron apoptosis, and in vivo silencing of RPS27A reduces neutrophil infiltration and improves outcomes in cerebral ischemia-reperfusion injury.\",\n      \"method\": \"siRNA knockdown, OGD/R model, MCAO model, cytokine assays, Western blot\",\n      \"journal\": \"Molecular medicine (Cambridge, Mass.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro and in vivo loss-of-function with defined pathway readout; single lab, two model systems\",\n      \"pmids\": [\"39069432\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ASFV protein pCP312R interacts with RPS27A (a component of the 40S ribosomal subunit), causing modification in the subcellular localization of RPS27A, which suppresses host protein translation. Knockout of RPS27A completely abolished the host protein shutoff activity of pCP312R.\",\n      \"method\": \"LC-MS/co-immunoprecipitation, crystal structure of pCP312R, confocal microscopy, Renilla-Glo luciferase assay, ribopuromycylation, RPS27A knockout/complementation\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — crystal structure of viral binding partner, Co-IP, genetic knockout with functional complementation, and multiple translation assays; multiple orthogonal methods\",\n      \"pmids\": [\"39069039\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Ubiquitin/ribosomal protein S27a was identified as an interacting protein of protein kinase CK2alpha' subunit by yeast two-hybrid screening of an HL-60 cell cDNA library.\",\n      \"method\": \"Yeast two-hybrid screening\",\n      \"journal\": \"Ai zheng = Aizheng = Chinese journal of cancer\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single yeast two-hybrid result, no validation by orthogonal method\",\n      \"pmids\": [\"15642198\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Structural analysis identified that the conserved structural motifs of bacterial ribosomal protein S16p that contact rRNA in the 30S subunit are present in eukaryotic ribosomal protein S27Ae (RPS27A), suggesting these families are homologous.\",\n      \"method\": \"Sequence alignment and comparative structural analysis with T. thermophilus 30S crystal structure\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational sequence/structural comparison, no direct experimental validation of rRNA contact for RPS27A\",\n      \"pmids\": [\"20034956\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"HucMSC-derived extracellular vesicles deliver RPS27A protein to neurons. RPS27A binds to the MDM2 promoter, promoting p53 ubiquitination and degradation, thereby exerting neuroprotective effects in Parkinson's disease models. MDM2 overexpression strengthened the therapeutic effect.\",\n      \"method\": \"EV co-culture, RPS27A silencing, chromatin immunoprecipitation (ChIP) for MDM2 promoter binding, MDM2 overexpression rescue, in vitro and in vivo PD models\",\n      \"journal\": \"Journal of neuroimmune pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP demonstrating RPS27A binding to MDM2 promoter, functional rescue with MDM2 overexpression; single lab\",\n      \"pmids\": [\"40338442\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RPS27A is a small 40S ribosomal subunit protein synthesized as a ubiquitin fusion precursor (Ub-RPS27a) that is co-translationally cleaved by deubiquitinases (including USP16, which also removes ubiquitin from an internal lysine of RPS27a to promote late 40S maturation); beyond its ribosomal role, RPS27A functions as an extraribosomal regulator of the MDM2-p53 axis by binding the MDM2 acidic domain to suppress MDM2-mediated p53 ubiquitination, while MDM2 reciprocally ubiquitinates RPS27A for proteasomal degradation; RPS27A also directly binds RPL11 to modulate RPL11-MDM2 interaction during ribosomal stress, undergoes nucleolar-to-nucleoplasm translocation to regulate p53 stability, antagonizes RNF168-mediated histone H2A ubiquitination at DNA damage sites through its C-terminal domain, is transcriptionally activated by p53 (forming a feedback loop) and by phospho-STAT3, and is ubiquitinated and degraded by the E3 ligase TRIM13 to suppress NF-κB signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPS27A is a structural protein of the small (40S) ribosomal subunit that is synthesized as a ubiquitin fusion precursor (Ub-RPS27a) and processed to release free ubiquitin and the 80-residue C2-C2 zinc-finger ribosomal protein [#0, #1]. During late cytoplasmic 40S maturation the deubiquitinase USP16 removes ubiquitin from an internal lysine of RPS27a/eS31 in a translation-dependent manner, and loss of USP16 causes 18S rRNA processing defects and impaired recycling of biogenesis factors [#8]; RPS27A itself is required for rRNA production across cell lines [#11]. Beyond the ribosome, RPS27A is an extraribosomal regulator of the MDM2–p53 axis: it binds the MDM2 central acidic domain to suppress MDM2-mediated p53 ubiquitination and drive p53 activation and cell-cycle arrest, while MDM2 reciprocally ubiquitinates RPS27A for proteasomal degradation [#3], and it directly binds RPL11 to tune the RPL11–MDM2 interaction during ribosomal stress [#10]. This regulation is coupled to nucleolar-to-nucleoplasm translocation of RPS27A that lowers MDM2 Ser166 phosphorylation and stabilizes p53 [#7, #13], and RPS27A is itself a direct p53 transcriptional target that amplifies the damage response [#5]. In the DNA-damage response RPS27A is recruited to lesions and, through its C-terminal ribosomal fragment, antagonizes RNF168-mediated H2A/H2AX K13/15 ubiquitination by masking the nucleosome acidic patch, impairing 53BP1 recruitment [#12]. RPS27A also controls NF-\\u03baB signaling, being targeted for degradation by the E3 ligase TRIM13 [#15] and acting through a PSMD12/NF-\\u03baB axis in microglia [#16]. RPS27A is exploited by multiple pathogens, whose proteins bind it to stabilize viral oncoproteins or to shut off host translation [#6, #17].\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 1989,\n      \"claim\": \"Established that the longer C-terminal extension of the ubiquitin fusion gene is a bona fide ribosomal protein, defining RPS27A's core identity as a 40S subunit component.\",\n      \"evidence\": \"Immunoblotting of rat 40S subunit protein fractions\",\n      \"pmids\": [\"2538756\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish rRNA contacts or assembly role\", \"Functional consequence of ribosomal incorporation not addressed\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Showed that the ubiquitin-S27a precursor is proteolytically processed to free ubiquitin plus an 80-aa zinc-finger protein, defining the precursor maturation step and RPS27A domain architecture.\",\n      \"evidence\": \"In vitro processing in reticulocyte lysate; recombinant cDNA characterization\",\n      \"pmids\": [\"7488009\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Protease responsible not identified\", \"Functional role of the C2-C2 zinc finger unresolved\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"First proposed a non-ribosomal partner by identifying RPS27A as a CK2alpha' interactor, raising the possibility of signaling roles.\",\n      \"evidence\": \"Yeast two-hybrid screen of HL-60 cDNA library\",\n      \"pmids\": [\"15642198\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Y2H hit with no orthogonal validation\", \"No functional consequence demonstrated\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Defined RPS27A as an extraribosomal regulator of p53 by mapping its binding to the MDM2 acidic domain and demonstrating a reciprocal MDM2-RPS27A regulatory loop.\",\n      \"evidence\": \"Co-IP, in vitro ubiquitination, shRNA knockdown, cell-cycle analysis under ribosomal stress\",\n      \"pmids\": [\"21561866\", \"22158882\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the acidic-domain interaction not resolved\", \"Trigger for the nucleolar release of RPS27A not defined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Placed RPS27A within a p53 feedback loop by showing it is a direct p53 transcriptional target required to amplify the p21 damage response.\",\n      \"evidence\": \"Reporter/runoff assay with dominant-negative p53 and RNAi, Western blot\",\n      \"pmids\": [\"25592822\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"p53 response element not finely mapped\", \"Cell-type generality not tested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Linked oncogenic signaling to RPS27A expression by demonstrating phospho-STAT3 transactivation through defined promoter elements.\",\n      \"evidence\": \"ChIP, promoter reporter, STAT3 inhibitor, Western blot in CML cells\",\n      \"pmids\": [\"26942564\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream consequence of elevated RPS27A in CML not mechanistically dissected\", \"Single cell context\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Connected drug-induced microtubule perturbation to p53 activation through nucleolar-to-nucleoplasm translocation of RPS27A and reduced MDM2 Ser166 phosphorylation.\",\n      \"evidence\": \"Immunofluorescence localization, Western blot, half-life assays; viral oncoprotein stabilization assays\",\n      \"pmids\": [\"28928040\", \"28735865\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular driver of translocation incompletely defined\", \"How RPS27A alters MDM2 phosphorylation not established\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Established the deubiquitination step in 40S maturation (USP16 removing ubiquitin from RPS27a) and showed DNA breaks deplete RPS27a from ribosomes to remodel translation.\",\n      \"evidence\": \"MS of trapped pre-40S, USP16 deletion with rRNA processing assay; ribosome profiling with Cas9/dCas9 controls and proteasome inhibition\",\n      \"pmids\": [\"32129764\", \"34914197\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"E3 ligase adding the internal ubiquitin not identified\", \"Translational targets remodeled after RPS27a loss not fully cataloged\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Refined the p53 mechanism by identifying direct RPS27A-RPL11 binding that gates RPL11-MDM2 interaction, and revealed cell-type-dependent p53 dependence on RPS27A.\",\n      \"evidence\": \"GST pull-down, Co-IP, in vitro ubiquitination, xenograft; systematic knockdown across multiple cell lines\",\n      \"pmids\": [\"35073964\", \"37371478\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Basis for cell-type variability in p53 response unexplained\", \"Stoichiometry of the RPS27A-RPL11-MDM2 assembly unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined a chromatin-level function in which the RPS27A C-terminal fragment masks the nucleosome acidic patch to antagonize RNF168 H2A ubiquitination and 53BP1 recruitment.\",\n      \"evidence\": \"Co-IP, laser micro-irradiation imaging, domain mapping, H2A ubiquitination and 53BP1 foci assays\",\n      \"pmids\": [\"37451480\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Regulation of RPS27A recruitment to damage sites not defined\", \"Relationship between this role and its ribosomal pool unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connected RPS27A to NF-\\u03baB control through TRIM13-mediated degradation and a PSMD12/NF-\\u03baB axis, and demonstrated pathogen hijacking for host translational shutoff.\",\n      \"evidence\": \"Co-IP and ubiquitination assays with NF-\\u03baB reporters and tumor models; ASFV pCP312R crystal structure, Co-IP, RPS27A knockout/complementation, translation assays\",\n      \"pmids\": [\"39667820\", \"39069432\", \"39069039\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct mechanism by which RPS27A modulates NF-\\u03baB not resolved\", \"Whether translational and signaling pools are distinct unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed RPS27A can act in trans, delivered by extracellular vesicles, binding the MDM2 promoter to promote p53 degradation and confer neuroprotection.\",\n      \"evidence\": \"EV co-culture, ChIP for MDM2 promoter binding, MDM2-overexpression rescue, PD models\",\n      \"pmids\": [\"40338442\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct DNA-binding activity of RPS27A at the MDM2 promoter not biochemically characterized\", \"Reconciliation with RPS27A's p53-stabilizing roles in other contexts unaddressed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RPS27A partitions between its ribosomal, p53-regulatory, chromatin, and NF-\\u03baB functions, and what governs its release from the nucleolus and ribosome, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model linking ribosomal incorporation to extraribosomal pools\", \"Signals controlling subcellular redistribution not defined\", \"Structural basis of MDM2/RPL11/nucleosome interactions incomplete\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 10, 12]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [20]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [0, 17]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [4, 7, 13]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [7, 13]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [12, 20]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [8, 11]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [9, 12]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [15, 16]}\n    ],\n    \"complexes\": [\"40S ribosomal subunit\"],\n    \"partners\": [\"MDM2\", \"RPL11\", \"USP16\", \"RNF168\", \"TRIM13\", \"PSMD12\", \"STAT3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":{"gene":"RPS27A","tier":"GROUNDING","verdict":"Evidence-grounding concern","subtype":"fabrication","uniprot_band":"rich","rules_fired":"R7","issue":"R7: fabricated (no corpus paper): 39069432"},"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}