{"gene":"RPL27A","run_date":"2026-06-10T07:46:26","timeline":{"discoveries":[{"year":2020,"finding":"RPL27A (uL15) carries a post-translational hydroxylation modification at His39 residue. Mutation of His39 to Ala or Thr in HEK293 cells reduced the translational activity of ribosomes by ~35% compared to wild-type uL15, establishing that this hydroxylation is required for full translational activity. Structural modeling suggests the hydroxyl group stabilizes local ribosome structure via a hydrogen bond with the imidazole ring of neighboring His40, near the E site of the ribosome.","method":"Cell-based mutagenesis (His39Ala, His39Thr, His40Ala substitutions) with functional complementation in HEK293 cells; translational activity assay; structural modeling of human ribosome","journal":"Molekuliarnaia biologiia","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cell-based complementation with mutant forms and functional readout in single lab, two methods (activity assay + structural modeling), but no in vitro reconstitution or crystal structure","pmids":["32492015"],"is_preprint":false},{"year":2023,"finding":"Mutation of His39 in RPL27A (uL15) to Ala (abolishing hydroxylation) causes specific changes in the translatome in HEK293T cells: ribosomes with the His39Ala mutant preferentially translate more abundant mRNAs with shorter coding sequences, while translation of longer and rarer mRNAs decreases. This demonstrates that hydroxylation at His39 of RPL27A contributes to ribosome heterogeneity and influences selective mRNA translation.","method":"Transient transfection of HEK293T cells with wild-type or His39Ala mutant uL15 constructs; RNA-seq of total cellular and polysome-associated mRNAs; differential gene expression analysis","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — polysome profiling combined with RNA-seq and mutagenesis in single lab, two orthogonal methods","pmids":["37047141"],"is_preprint":false},{"year":2023,"finding":"Martynoside (MAR) directly binds RPL27A at the region encoded by exons 4 and 5. MAR binding increases RPL27A protein stability by reducing ubiquitination at Lys92 (K92) and Lys94 (K94). Disruption of the MAR-binding residues in RPL27A abolished MAR-induced stabilization. MAR-mediated stabilization of RPL27A rescued 5-FU-impaired ribosome biogenesis, restoring mature rRNA abundance, ribosomal protein levels, ribosome assembly, and nucleolar integrity.","method":"mRNA display with library of even-distribution (md-LED) in vitro binding screen; structural and mutational analysis; label-free quantitative ubiquitination proteomics; transcriptomics; ribosome function assays; Western blot","journal":"Science bulletin","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro direct binding identification combined with structural/mutational validation, ubiquitination proteomics, and ribosome functional assays, multiple orthogonal methods in single study","pmids":["37481436"],"is_preprint":false},{"year":2011,"finding":"A mutation in the mouse Rpl27a gene (sooty foot ataxia mice) activates the p53 tumour suppressor pathway in vivo, causing cerebellar ataxia, pancytopenia, and epidermal hyperpigmentation. These phenotypes are rescued in a p53 haploinsufficient background. Reduced Rpl27a leads to decreased haematopoietic stem cells and p53-dependent c-Kit downregulation, placing Rpl27a upstream of p53 activation in ribosomal stress.","method":"ENU mutagenesis screen; genetic epistasis (Rpl27a mutant crossed to p53 heterozygous mice); bone marrow analysis; immunophenotyping","journal":"The Journal of pathology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with p53 rescue, multiple phenotypic readouts, in vivo mouse model with rigorous controls","pmids":["21674502"],"is_preprint":false},{"year":2020,"finding":"In mouse spermatogonia, radiation-induced DNA damage reduces Rpl27a expression. Rpl27a reduction weakens binding of E2F1 and p53 to MDM2, causing p53 activation and E2F1 degradation. Co-transfection of ATM and Rpl27a or ATM inhibition could restore Rpl27a expression after carbon ion radiation, placing Rpl27a downstream of ATM-mediated DNA damage signaling and upstream of MDM2-p53/E2F1 pathway.","method":"In vivo carbon ion irradiation of mice; comparative proteomics and transcriptomics; immunofluorescence; co-transfection experiments in GC-1 cells; ATM inhibition; p53 knockout mouse model","journal":"Ecotoxicology and environmental safety","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple methods (proteomics, transcriptomics, co-transfection, genetic knockout) in single lab establishing pathway placement","pmids":["32535367"],"is_preprint":false},{"year":2016,"finding":"RPL27A is a direct target of miR-595. Knockdown of RPL27A induces p53 activation, apoptosis, and inhibition of proliferation. RPL27A knockdown also disrupts 60S ribosome subunit biogenesis and nucleolar integrity. In normal CD34+ cells, RPL27A knockdown preferentially blocks erythroid proliferation and differentiation. RPL27A overexpression enhances cellular proliferation without significantly affecting p53 mRNA levels, suggesting p53 protein-level (not transcriptional) regulation.","method":"Luciferase reporter gene assay (miR-595 targeting); RPL27A knockdown and overexpression experiments; Western blot; ribosome subunit analysis; differentiation assays in CD34+ cells","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — luciferase reporter confirms direct targeting, loss-of-function with multiple cellular readouts, single lab","pmids":["27374104"],"is_preprint":false},{"year":2022,"finding":"RPL27A is a downstream target of tRF-19-W4PU732S in breast cancer cells. Knockdown of RPL27A partially restored the promoting effects of tRF-19-W4PU732S on BC cell viability, invasion, migration, EMT markers (OCT-4A, SOX2, Vimentin upregulation; E-cadherin downregulation), cancer stem-like cell phenotypes, and suppression of apoptosis, establishing RPL27A as a mediator of these processes.","method":"Luciferase reporter assay; Western blot; siRNA knockdown of RPL27A; rescue experiments; cell proliferation, migration, invasion assays; apoptosis assays","journal":"Bioengineered","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, reporter assay and knockdown with cellular phenotype readouts, no direct molecular mechanism for RPL27A's specific contribution established","pmids":["35030975"],"is_preprint":false},{"year":1990,"finding":"Rat ribosomal protein L27a (ortholog of human RPL27A) contains 147 amino acids (after N-terminal methionine removal) with molecular weight 16,476 Da and is a component of the 60S ribosomal large subunit. The N-terminal methionine is removed post-translationally. The gene is present in 18-22 copies in nuclear DNA, and the mRNA is approximately 600 nucleotides in length.","method":"Protein sequencing from recombinant cDNA; N-terminal amino acid sequencing; Southern blot hybridization; Northern blot","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — direct protein sequencing confirmed by N-terminal amino acid analysis, foundational biochemical characterization","pmids":["2207170"],"is_preprint":false},{"year":1999,"finding":"The human RPL27A gene (and mouse Rpl27a) contains a specific exon/intron structure where the translational start codon ATG is separated from the main reading frame by the first intron. The promoter region lacks a canonical TATA box but contains Sp1 binding sites, a pyrimidine cluster, and transcriptional regulatory elements Box-A and GABP, located within a CpG island, characteristic of ribosomal protein genes. The human gene maps to chromosome 11p15.","method":"Gene cloning and sequencing; FISH; promoter analysis","journal":"Cytogenetics and cell genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct cloning, sequencing and FISH localization with functional regulatory element identification","pmids":["10449908"],"is_preprint":false},{"year":2021,"finding":"Knockdown of RPL27A in the TNBC cell line MDA-MB-231 significantly reduced cell migration and invasion, establishing a functional role for RPL27A in cancer cell motility. This was identified in the context of EIF2 signaling pathway activation in metastatic TNBC.","method":"siRNA knockdown of RPL27A; in vitro cell migration and invasion assays; single-cell RNA-seq analysis","journal":"Frontiers in cell and developmental biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, knockdown with cell phenotype readout, no molecular mechanism for RPL27A's specific role established","pmids":["34497807"],"is_preprint":false}],"current_model":"RPL27A (uL15) is a component of the 60S ribosomal large subunit that carries a post-translational hydroxylation at His39 near the E-site of the ribosome, which is required for full translational activity and influences selective mRNA translation; it is subject to ubiquitination-mediated degradation (at K92/K94) and can be stabilized by direct ligand binding; reduced RPL27A levels trigger ribosomal stress, activating p53 through the MDM2 pathway in multiple tissues, and RPL27A plays a role in ribosome biogenesis, nucleolar integrity, and erythroid differentiation."},"narrative":{"mechanistic_narrative":"RPL27A (uL15) is a structural protein of the 60S ribosomal large subunit that contributes to translational competence and ribosome biogenesis, and acts as a sensor coupling ribosomal integrity to the p53 stress response [PMID:2207170, PMID:27374104, PMID:21674502]. The protein carries a post-translational hydroxylation at His39 located near the ribosomal E-site, which stabilizes local structure through a hydrogen bond with neighboring His40 and is required for full translational activity; loss of this modification reshapes the translatome toward abundant mRNAs with shorter coding sequences, establishing a role in ribosome heterogeneity and selective mRNA translation [PMID:32492015, PMID:37047141]. RPL27A protein stability is governed by ubiquitination at Lys92 and Lys94, and direct ligand binding (martynoside) at the exon 4/5-encoded region reduces this ubiquitination, stabilizing the protein and restoring impaired ribosome biogenesis, mature rRNA abundance, ribosome assembly, and nucleolar integrity [PMID:37481436]. Reduced RPL27A levels disrupt 60S subunit biogenesis and nucleolar integrity and trigger ribosomal stress that activates p53 at the protein level through the MDM2 pathway, with consequences including blocked erythroid proliferation/differentiation, hematopoietic stem cell loss, cerebellar ataxia, and pancytopenia in vivo, all rescuable by reducing p53 dosage [PMID:27374104, PMID:21674502, PMID:32535367]. In DNA-damage signaling, RPL27A is reduced downstream of ATM and weakens E2F1/p53 binding to MDM2, positioning it upstream of MDM2-p53/E2F1 control [PMID:32535367].","teleology":[{"year":1990,"claim":"Established the basic identity of RPL27A (L27a) as a small basic protein of the 60S large ribosomal subunit, providing the foundational biochemical anchor for all later functional work.","evidence":"Protein sequencing of rat L27a from recombinant cDNA, N-terminal sequencing, Southern and Northern blot","pmids":["2207170"],"confidence":"Medium","gaps":["No human protein characterized directly","No position within 60S architecture defined","No functional or regulatory role addressed"]},{"year":1999,"claim":"Defined the genomic and promoter architecture of human RPL27A, showing it has the TATA-less, Sp1/CpG-island regulatory features typical of ribosomal protein genes and mapping it to 11p15.","evidence":"Gene cloning, sequencing, FISH, and promoter analysis","pmids":["10449908"],"confidence":"Medium","gaps":["Transcriptional regulators not functionally validated","No link from gene structure to protein function","Splicing requirement (ATG separated by intron 1) not mechanistically tested"]},{"year":2011,"claim":"Placed RPL27A genetically upstream of p53 in ribosomal stress in vivo, showing that reduced RPL27A causes ataxia, pancytopenia, and hematopoietic defects that are p53-dependent.","evidence":"ENU mutagenesis sooty foot ataxia mouse, genetic epistasis with p53 heterozygosity, bone marrow/immunophenotyping","pmids":["21674502"],"confidence":"High","gaps":["Molecular mechanism linking RPL27A loss to p53 activation not resolved","Whether ribosome biogenesis defect is the trigger not directly shown","c-Kit downregulation mechanism beyond p53-dependence undefined"]},{"year":2016,"claim":"Connected RPL27A loss to specific cellular outcomes—disrupted 60S biogenesis, nucleolar disintegration, protein-level p53 activation, apoptosis, and blocked erythroid differentiation—identifying it as a miR-595 target.","evidence":"miR-595 luciferase reporter, RPL27A knockdown/overexpression, ribosome subunit analysis, CD34+ differentiation assays","pmids":["27374104"],"confidence":"Medium","gaps":["Direct biochemical step from biogenesis defect to MDM2/p53 not mapped","Erythroid specificity mechanism unexplained","No reciprocal validation of the biogenesis vs. p53 ordering"]},{"year":2020,"claim":"Identified a functional post-translational hydroxylation at His39 required for full ribosomal translational activity, giving the protein a role beyond passive structure.","evidence":"His39Ala/Thr and His40Ala mutagenesis with functional complementation and translation activity assay in HEK293 plus structural modeling","pmids":["32492015"],"confidence":"Medium","gaps":["Hydroxylating enzyme not identified","No crystal structure or in vitro reconstitution","Stoichiometry and regulation of hydroxylation unknown"]},{"year":2020,"claim":"Positioned Rpl27a within ATM-mediated DNA-damage signaling, showing radiation reduces Rpl27a and that this loss alters E2F1/p53 binding to MDM2.","evidence":"In vivo carbon-ion irradiation, proteomics/transcriptomics, GC-1 co-transfection, ATM inhibition, p53 knockout mice","pmids":["32535367"],"confidence":"Medium","gaps":["Direct physical interactions at MDM2 not demonstrated","Mechanism by which RPL27A modulates MDM2 binding unclear","Generality beyond spermatogonia untested"]},{"year":2023,"claim":"Demonstrated that His39 hydroxylation tunes selective mRNA translation, establishing RPL27A as a contributor to ribosome heterogeneity rather than a uniform structural component.","evidence":"His39Ala mutant transfection with polysome profiling and RNA-seq differential analysis in HEK293T","pmids":["37047141"],"confidence":"Medium","gaps":["Features determining mRNA selectivity not defined","Physiological contexts where this matters unknown","Link to specific cellular phenotypes not established"]},{"year":2023,"claim":"Defined the post-translational stability control of RPL27A, showing K92/K94 ubiquitination drives degradation and that direct ligand binding at exons 4/5 stabilizes the protein and rescues impaired ribosome biogenesis.","evidence":"md-LED in vitro binding screen with martynoside, mutational mapping, ubiquitination proteomics, rRNA/ribosome assembly and nucleolar integrity assays","pmids":["37481436"],"confidence":"High","gaps":["Endogenous E3 ligase and deubiquitinase not identified","Physiological ligand (if any) unknown","Whether stabilization affects p53 axis not tested"]},{"year":2022,"claim":"Implicated RPL27A as a downstream mediator of an oncogenic tRNA fragment in breast cancer EMT and stemness phenotypes.","evidence":"Luciferase reporter, siRNA knockdown and rescue, migration/invasion/apoptosis and EMT marker assays","pmids":["35030975"],"confidence":"Low","gaps":["No direct molecular mechanism for RPL27A's specific contribution established","Reporter/knockdown correlative only","Not independently validated"]},{"year":2021,"claim":"Associated RPL27A with cancer cell motility in triple-negative breast cancer in the context of EIF2 signaling.","evidence":"siRNA knockdown with migration/invasion assays and single-cell RNA-seq in MDA-MB-231","pmids":["34497807"],"confidence":"Low","gaps":["No molecular mechanism for the motility phenotype","EIF2 link correlative","Knockdown effects may reflect general ribosome loss"]},{"year":null,"claim":"The enzyme that installs the His39 hydroxyl, the endogenous E3 ligase/DUB controlling K92/K94 ubiquitination, and the direct biochemical step connecting RPL27A loss to MDM2-p53 activation remain unidentified.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No hydroxylase identified","No endogenous ubiquitination machinery defined","Direct molecular link between ribosomal stress and MDM2/p53 not reconstituted"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[7,0]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[7,0]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[2,5]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,2]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[2,5]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[3,4]}],"complexes":["60S ribosomal large subunit"],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P46776","full_name":"Large ribosomal subunit protein uL15","aliases":["60S ribosomal protein L27a"],"length_aa":148,"mass_kda":16.6,"function":"Component of the large ribosomal subunit (PubMed:23636399, PubMed:32669547). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:23636399, PubMed:32669547)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P46776/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPL27A","classification":"Common Essential","n_dependent_lines":1208,"n_total_lines":1208,"dependency_fraction":1.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPRIN1","stoichiometry":10.0},{"gene":"DRG1","stoichiometry":10.0},{"gene":"EIF2S3","stoichiometry":10.0},{"gene":"EIF3B","stoichiometry":10.0},{"gene":"ENY2","stoichiometry":10.0},{"gene":"RACK1","stoichiometry":10.0},{"gene":"RBM8A","stoichiometry":10.0},{"gene":"RPL11","stoichiometry":10.0},{"gene":"RPL13","stoichiometry":10.0},{"gene":"RPL4","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/RPL27A","total_profiled":1310},"omim":[{"mim_id":"611333","title":"SMALL NUCLEOLAR RNA, H/ACA BOX, 3B; SNORA3B","url":"https://www.omim.org/entry/611333"},{"mim_id":"603638","title":"RIBOSOMAL PROTEIN L28; RPL28","url":"https://www.omim.org/entry/603638"},{"mim_id":"603637","title":"RIBOSOMAL PROTEIN L27a; RPL27A","url":"https://www.omim.org/entry/603637"},{"mim_id":"603636","title":"RIBOSOMAL PROTEIN L21; RPL21","url":"https://www.omim.org/entry/603636"},{"mim_id":"603634","title":"RIBOSOMAL PROTEIN L5; RPL5","url":"https://www.omim.org/entry/603634"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Endoplasmic reticulum","reliability":"Enhanced"},{"location":"Cytosol","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPL27A"},"hgnc":{"alias_symbol":["L27A","uL15"],"prev_symbol":[]},"alphafold":{"accession":"P46776","domains":[{"cath_id":"-","chopping":"29-58","consensus_level":"medium","plddt":96.5567,"start":29,"end":58},{"cath_id":"3.100.10.10","chopping":"65-145","consensus_level":"high","plddt":92.0596,"start":65,"end":145}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P46776","model_url":"https://alphafold.ebi.ac.uk/files/AF-P46776-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P46776-F1-predicted_aligned_error_v6.png","plddt_mean":93.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPL27A","jax_strain_url":"https://www.jax.org/strain/search?query=RPL27A"},"sequence":{"accession":"P46776","fasta_url":"https://rest.uniprot.org/uniprotkb/P46776.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P46776/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P46776"}},"corpus_meta":[{"pmid":"7966602","id":"PMC_7966602","title":"The herpes simplex virus 1 UL15 gene encodes two proteins and is required for cleavage of genomic viral DNA.","date":"1994","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/7966602","citation_count":88,"is_preprint":false},{"pmid":"8331721","id":"PMC_8331721","title":"Characterization of a temperature-sensitive mutant of the UL15 open reading frame of herpes simplex virus 1.","date":"1993","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/8331721","citation_count":88,"is_preprint":false},{"pmid":"9696839","id":"PMC_9696839","title":"Herpes simplex virus type 1 cleavage and packaging proteins UL15 and UL28 are associated with B but not C capsids during packaging.","date":"1998","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/9696839","citation_count":78,"is_preprint":false},{"pmid":"9060619","id":"PMC_9060619","title":"The U(L)15 gene of herpes simplex virus type 1 contains within its second exon a novel open reading frame that is translated in frame with the U(L)15 gene product.","date":"1997","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/9060619","citation_count":75,"is_preprint":false},{"pmid":"11967295","id":"PMC_11967295","title":"DNA cleavage and packaging proteins encoded by genes U(L)28, U(L)15, and U(L)33 of herpes simplex virus type 1 form a complex in infected cells.","date":"2002","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/11967295","citation_count":69,"is_preprint":false},{"pmid":"7772601","id":"PMC_7772601","title":"Cloning, sequencing and expression of the L5, L21, L27a, L28, S5, S9, S10 and S29 human ribosomal protein mRNAs.","date":"1995","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/7772601","citation_count":66,"is_preprint":false},{"pmid":"9882384","id":"PMC_9882384","title":"Physical and functional interactions between the herpes simplex virus UL15 and UL28 DNA cleavage and packaging proteins.","date":"1999","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/9882384","citation_count":57,"is_preprint":false},{"pmid":"12743292","id":"PMC_12743292","title":"Herpes simplex virus type 1 portal protein UL6 interacts with the putative terminase subunits UL15 and UL28.","date":"2003","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/12743292","citation_count":56,"is_preprint":false},{"pmid":"9060618","id":"PMC_9060618","title":"Characterization of ICP6::lacZ insertion mutants of the UL15 gene of herpes simplex virus type 1 reveals the translation of two proteins.","date":"1997","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/9060618","citation_count":53,"is_preprint":false},{"pmid":"1333128","id":"PMC_1333128","title":"The virulence-determining genomic BamHI fragment 4 of pseudorabies virus contains genes corresponding to the UL15 (partial), UL18, UL19, UL20, and UL21 genes of herpes simplex virus and a putative origin of replication.","date":"1992","source":"Virology","url":"https://pubmed.ncbi.nlm.nih.gov/1333128","citation_count":45,"is_preprint":false},{"pmid":"11086131","id":"PMC_11086131","title":"Interaction of the herpes simplex virus type 1 packaging protein UL15 with full-length and deleted forms of the UL28 protein.","date":"2000","source":"The Journal of general virology","url":"https://pubmed.ncbi.nlm.nih.gov/11086131","citation_count":41,"is_preprint":false},{"pmid":"9371568","id":"PMC_9371568","title":"The pseudorabies virus UL28 protein enters the nucleus after coexpression with the herpes simplex virus UL15 protein.","date":"1997","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/9371568","citation_count":39,"is_preprint":false},{"pmid":"12915573","id":"PMC_12915573","title":"Point mutations in exon I of the herpes simplex virus putative terminase subunit, UL15, indicate that the most conserved residues are essential for cleavage and packaging.","date":"2003","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/12915573","citation_count":37,"is_preprint":false},{"pmid":"24872379","id":"PMC_24872379","title":"Ribosomal Protein RPL27a Promotes Female Gametophyte Development in a Dose-Dependent Manner.","date":"2014","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/24872379","citation_count":35,"is_preprint":false},{"pmid":"16920825","id":"PMC_16920825","title":"Herpes simplex virus 1 DNA packaging proteins encoded by UL6, UL15, UL17, UL28, and UL33 are located on the external surface of the viral capsid.","date":"2006","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/16920825","citation_count":35,"is_preprint":false},{"pmid":"35030975","id":"PMC_35030975","title":"tRF-19-W4PU732S promotes breast cancer cell malignant activity by targeting inhibition of RPL27A (ribosomal protein-L27A).","date":"2022","source":"Bioengineered","url":"https://pubmed.ncbi.nlm.nih.gov/35030975","citation_count":33,"is_preprint":false},{"pmid":"34497807","id":"PMC_34497807","title":"Ribosome Proteins Represented by RPL27A Mark the Development and Metastasis of Triple-Negative Breast Cancer in Mouse and Human.","date":"2021","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/34497807","citation_count":31,"is_preprint":false},{"pmid":"17035316","id":"PMC_17035316","title":"Linker insertion mutations in the herpes simplex virus type 1 UL28 gene: effects on UL28 interaction with UL15 and UL33 and identification of a second-site mutation in the UL15 gene that suppresses a lethal UL28 mutation.","date":"2006","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/17035316","citation_count":29,"is_preprint":false},{"pmid":"21674502","id":"PMC_21674502","title":"Rpl27a mutation in the sooty foot ataxia mouse phenocopies high p53 mouse models.","date":"2011","source":"The Journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/21674502","citation_count":25,"is_preprint":false},{"pmid":"1323715","id":"PMC_1323715","title":"The cDNA of UL15, a highly conserved herpes simplex virus 1 gene, effectively replaces the two exons of the wild-type virus.","date":"1992","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/1323715","citation_count":25,"is_preprint":false},{"pmid":"1656627","id":"PMC_1656627","title":"Sequence analysis of the splice junction in the transcript of herpes simplex virus type 1 gene UL15.","date":"1991","source":"Virus research","url":"https://pubmed.ncbi.nlm.nih.gov/1656627","citation_count":25,"is_preprint":false},{"pmid":"2207170","id":"PMC_2207170","title":"The primary structure of rat ribosomal proteins: the amino acid sequences of L27a and L28 and corrections in the sequences of S4 and S12.","date":"1990","source":"Biochimica et biophysica 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dysgenesis.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/27374104","citation_count":22,"is_preprint":false},{"pmid":"21880766","id":"PMC_21880766","title":"A mutation in UL15 of herpes simplex virus 1 that reduces packaging of cleaved genomes.","date":"2011","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/21880766","citation_count":20,"is_preprint":false},{"pmid":"10482584","id":"PMC_10482584","title":"Proteolytic cleavage of the amino terminus of the U(L)15 gene product of herpes simplex virus type 1 is coupled with maturation of viral DNA into unit-length genomes.","date":"1999","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/10482584","citation_count":20,"is_preprint":false},{"pmid":"32535367","id":"PMC_32535367","title":"Heavy ion radiation-induced DNA damage mediates apoptosis via the Rpl27a-Rpl5-MDM2-p53/E2F1 signaling pathway in mouse spermatogonia.","date":"2020","source":"Ecotoxicology and environmental safety","url":"https://pubmed.ncbi.nlm.nih.gov/32535367","citation_count":19,"is_preprint":false},{"pmid":"21448008","id":"PMC_21448008","title":"Involvement of ribosomal protein RPL27a in meristem activity and organ development.","date":"2011","source":"Plant signaling & behavior","url":"https://pubmed.ncbi.nlm.nih.gov/21448008","citation_count":17,"is_preprint":false},{"pmid":"21251324","id":"PMC_21251324","title":"Distribution of allele frequencies at TTN g.231054C > T, RPL27A g.3109537C > T and AKIRIN2 c.*188G > A between Japanese Black and four other cattle breeds with differing historical selection for marbling.","date":"2011","source":"BMC research notes","url":"https://pubmed.ncbi.nlm.nih.gov/21251324","citation_count":12,"is_preprint":false},{"pmid":"37481436","id":"PMC_37481436","title":"Martynoside rescues 5-fluorouracil-impaired ribosome biogenesis by stabilizing RPL27A.","date":"2023","source":"Science bulletin","url":"https://pubmed.ncbi.nlm.nih.gov/37481436","citation_count":10,"is_preprint":false},{"pmid":"20163651","id":"PMC_20163651","title":"Association of a single nucleotide polymorphism in ribosomal protein L27a gene with marbling in Japanese Black beef cattle.","date":"2009","source":"Animal science journal = Nihon chikusan Gakkaiho","url":"https://pubmed.ncbi.nlm.nih.gov/20163651","citation_count":10,"is_preprint":false},{"pmid":"8297386","id":"PMC_8297386","title":"The Drosophila melanogaster homolog of ribosomal protein L27a.","date":"1994","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/8297386","citation_count":7,"is_preprint":false},{"pmid":"21466705","id":"PMC_21466705","title":"Identification of a spliced gene from duck enteritis virus encoding a protein homologous to UL15 of herpes simplex virus 1.","date":"2011","source":"Virology 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biologiia","url":"https://pubmed.ncbi.nlm.nih.gov/32492015","citation_count":6,"is_preprint":false},{"pmid":"37047141","id":"PMC_37047141","title":"Mutation at the Site of Hydroxylation in the Ribosomal Protein uL15 (RPL27a) Causes Specific Changes in the Repertoire of mRNAs Translated in Mammalian Cells.","date":"2023","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/37047141","citation_count":4,"is_preprint":false},{"pmid":"9836437","id":"PMC_9836437","title":"The characterization of two Dictyostelium discoideum genes encoding ribosomal proteins with sequence similarity to rat L27a and L37a.","date":"1998","source":"Bioscience, biotechnology, and biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9836437","citation_count":4,"is_preprint":false},{"pmid":"9055824","id":"PMC_9055824","title":"Cloning and sequencing of ribosomal protein L27a and a gene similar to human GS1 in Drosophila.","date":"1997","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/9055824","citation_count":3,"is_preprint":false},{"pmid":"10404268","id":"PMC_10404268","title":"Analysis of the 60 S ribosomal protein L27a (L29) gene of Trypanosoma brucei.","date":"1999","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/10404268","citation_count":3,"is_preprint":false},{"pmid":"41150132","id":"PMC_41150132","title":"Duck Plague Virus Full-Length UL15 Protein Is a Multifunctional Enzyme Which Not Only Possesses Nuclease Activity but Also Exerts ATPase and DNA-Binding Activity.","date":"2025","source":"Veterinary sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41150132","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.11.20.624617","title":"Characterization of the Kaposi’s sarcoma-associated herpesvirus terminase complex component ORF29","date":"2024-11-21","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.20.624617","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.06.23.661225","title":"A single-cell atlas of ribosomal protein heterogeneity across human tissues reveals phenotypes of biological and clinical significance","date":"2025-06-27","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.23.661225","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":23112,"output_tokens":2912,"usd":0.056508,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10230,"output_tokens":3454,"usd":0.06875,"stage2_stop_reason":"end_turn"},"total_usd":0.125258,"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\": 2020,\n      \"finding\": \"RPL27A (uL15) carries a post-translational hydroxylation modification at His39 residue. Mutation of His39 to Ala or Thr in HEK293 cells reduced the translational activity of ribosomes by ~35% compared to wild-type uL15, establishing that this hydroxylation is required for full translational activity. Structural modeling suggests the hydroxyl group stabilizes local ribosome structure via a hydrogen bond with the imidazole ring of neighboring His40, near the E site of the ribosome.\",\n      \"method\": \"Cell-based mutagenesis (His39Ala, His39Thr, His40Ala substitutions) with functional complementation in HEK293 cells; translational activity assay; structural modeling of human ribosome\",\n      \"journal\": \"Molekuliarnaia biologiia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-based complementation with mutant forms and functional readout in single lab, two methods (activity assay + structural modeling), but no in vitro reconstitution or crystal structure\",\n      \"pmids\": [\"32492015\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Mutation of His39 in RPL27A (uL15) to Ala (abolishing hydroxylation) causes specific changes in the translatome in HEK293T cells: ribosomes with the His39Ala mutant preferentially translate more abundant mRNAs with shorter coding sequences, while translation of longer and rarer mRNAs decreases. This demonstrates that hydroxylation at His39 of RPL27A contributes to ribosome heterogeneity and influences selective mRNA translation.\",\n      \"method\": \"Transient transfection of HEK293T cells with wild-type or His39Ala mutant uL15 constructs; RNA-seq of total cellular and polysome-associated mRNAs; differential gene expression analysis\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — polysome profiling combined with RNA-seq and mutagenesis in single lab, two orthogonal methods\",\n      \"pmids\": [\"37047141\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Martynoside (MAR) directly binds RPL27A at the region encoded by exons 4 and 5. MAR binding increases RPL27A protein stability by reducing ubiquitination at Lys92 (K92) and Lys94 (K94). Disruption of the MAR-binding residues in RPL27A abolished MAR-induced stabilization. MAR-mediated stabilization of RPL27A rescued 5-FU-impaired ribosome biogenesis, restoring mature rRNA abundance, ribosomal protein levels, ribosome assembly, and nucleolar integrity.\",\n      \"method\": \"mRNA display with library of even-distribution (md-LED) in vitro binding screen; structural and mutational analysis; label-free quantitative ubiquitination proteomics; transcriptomics; ribosome function assays; Western blot\",\n      \"journal\": \"Science bulletin\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro direct binding identification combined with structural/mutational validation, ubiquitination proteomics, and ribosome functional assays, multiple orthogonal methods in single study\",\n      \"pmids\": [\"37481436\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"A mutation in the mouse Rpl27a gene (sooty foot ataxia mice) activates the p53 tumour suppressor pathway in vivo, causing cerebellar ataxia, pancytopenia, and epidermal hyperpigmentation. These phenotypes are rescued in a p53 haploinsufficient background. Reduced Rpl27a leads to decreased haematopoietic stem cells and p53-dependent c-Kit downregulation, placing Rpl27a upstream of p53 activation in ribosomal stress.\",\n      \"method\": \"ENU mutagenesis screen; genetic epistasis (Rpl27a mutant crossed to p53 heterozygous mice); bone marrow analysis; immunophenotyping\",\n      \"journal\": \"The Journal of pathology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with p53 rescue, multiple phenotypic readouts, in vivo mouse model with rigorous controls\",\n      \"pmids\": [\"21674502\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In mouse spermatogonia, radiation-induced DNA damage reduces Rpl27a expression. Rpl27a reduction weakens binding of E2F1 and p53 to MDM2, causing p53 activation and E2F1 degradation. Co-transfection of ATM and Rpl27a or ATM inhibition could restore Rpl27a expression after carbon ion radiation, placing Rpl27a downstream of ATM-mediated DNA damage signaling and upstream of MDM2-p53/E2F1 pathway.\",\n      \"method\": \"In vivo carbon ion irradiation of mice; comparative proteomics and transcriptomics; immunofluorescence; co-transfection experiments in GC-1 cells; ATM inhibition; p53 knockout mouse model\",\n      \"journal\": \"Ecotoxicology and environmental safety\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple methods (proteomics, transcriptomics, co-transfection, genetic knockout) in single lab establishing pathway placement\",\n      \"pmids\": [\"32535367\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RPL27A is a direct target of miR-595. Knockdown of RPL27A induces p53 activation, apoptosis, and inhibition of proliferation. RPL27A knockdown also disrupts 60S ribosome subunit biogenesis and nucleolar integrity. In normal CD34+ cells, RPL27A knockdown preferentially blocks erythroid proliferation and differentiation. RPL27A overexpression enhances cellular proliferation without significantly affecting p53 mRNA levels, suggesting p53 protein-level (not transcriptional) regulation.\",\n      \"method\": \"Luciferase reporter gene assay (miR-595 targeting); RPL27A knockdown and overexpression experiments; Western blot; ribosome subunit analysis; differentiation assays in CD34+ cells\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — luciferase reporter confirms direct targeting, loss-of-function with multiple cellular readouts, single lab\",\n      \"pmids\": [\"27374104\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RPL27A is a downstream target of tRF-19-W4PU732S in breast cancer cells. Knockdown of RPL27A partially restored the promoting effects of tRF-19-W4PU732S on BC cell viability, invasion, migration, EMT markers (OCT-4A, SOX2, Vimentin upregulation; E-cadherin downregulation), cancer stem-like cell phenotypes, and suppression of apoptosis, establishing RPL27A as a mediator of these processes.\",\n      \"method\": \"Luciferase reporter assay; Western blot; siRNA knockdown of RPL27A; rescue experiments; cell proliferation, migration, invasion assays; apoptosis assays\",\n      \"journal\": \"Bioengineered\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, reporter assay and knockdown with cellular phenotype readouts, no direct molecular mechanism for RPL27A's specific contribution established\",\n      \"pmids\": [\"35030975\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"Rat ribosomal protein L27a (ortholog of human RPL27A) contains 147 amino acids (after N-terminal methionine removal) with molecular weight 16,476 Da and is a component of the 60S ribosomal large subunit. The N-terminal methionine is removed post-translationally. The gene is present in 18-22 copies in nuclear DNA, and the mRNA is approximately 600 nucleotides in length.\",\n      \"method\": \"Protein sequencing from recombinant cDNA; N-terminal amino acid sequencing; Southern blot hybridization; Northern blot\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — direct protein sequencing confirmed by N-terminal amino acid analysis, foundational biochemical characterization\",\n      \"pmids\": [\"2207170\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"The human RPL27A gene (and mouse Rpl27a) contains a specific exon/intron structure where the translational start codon ATG is separated from the main reading frame by the first intron. The promoter region lacks a canonical TATA box but contains Sp1 binding sites, a pyrimidine cluster, and transcriptional regulatory elements Box-A and GABP, located within a CpG island, characteristic of ribosomal protein genes. The human gene maps to chromosome 11p15.\",\n      \"method\": \"Gene cloning and sequencing; FISH; promoter analysis\",\n      \"journal\": \"Cytogenetics and cell genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct cloning, sequencing and FISH localization with functional regulatory element identification\",\n      \"pmids\": [\"10449908\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Knockdown of RPL27A in the TNBC cell line MDA-MB-231 significantly reduced cell migration and invasion, establishing a functional role for RPL27A in cancer cell motility. This was identified in the context of EIF2 signaling pathway activation in metastatic TNBC.\",\n      \"method\": \"siRNA knockdown of RPL27A; in vitro cell migration and invasion assays; single-cell RNA-seq analysis\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, knockdown with cell phenotype readout, no molecular mechanism for RPL27A's specific role established\",\n      \"pmids\": [\"34497807\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RPL27A (uL15) is a component of the 60S ribosomal large subunit that carries a post-translational hydroxylation at His39 near the E-site of the ribosome, which is required for full translational activity and influences selective mRNA translation; it is subject to ubiquitination-mediated degradation (at K92/K94) and can be stabilized by direct ligand binding; reduced RPL27A levels trigger ribosomal stress, activating p53 through the MDM2 pathway in multiple tissues, and RPL27A plays a role in ribosome biogenesis, nucleolar integrity, and erythroid differentiation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPL27A (uL15) is a structural protein of the 60S ribosomal large subunit that contributes to translational competence and ribosome biogenesis, and acts as a sensor coupling ribosomal integrity to the p53 stress response [#7, #5, #3]. The protein carries a post-translational hydroxylation at His39 located near the ribosomal E-site, which stabilizes local structure through a hydrogen bond with neighboring His40 and is required for full translational activity; loss of this modification reshapes the translatome toward abundant mRNAs with shorter coding sequences, establishing a role in ribosome heterogeneity and selective mRNA translation [#0, #1]. RPL27A protein stability is governed by ubiquitination at Lys92 and Lys94, and direct ligand binding (martynoside) at the exon 4/5-encoded region reduces this ubiquitination, stabilizing the protein and restoring impaired ribosome biogenesis, mature rRNA abundance, ribosome assembly, and nucleolar integrity [#2]. Reduced RPL27A levels disrupt 60S subunit biogenesis and nucleolar integrity and trigger ribosomal stress that activates p53 at the protein level through the MDM2 pathway, with consequences including blocked erythroid proliferation/differentiation, hematopoietic stem cell loss, cerebellar ataxia, and pancytopenia in vivo, all rescuable by reducing p53 dosage [#5, #3, #4]. In DNA-damage signaling, RPL27A is reduced downstream of ATM and weakens E2F1/p53 binding to MDM2, positioning it upstream of MDM2-p53/E2F1 control [#4].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 1990,\n      \"claim\": \"Established the basic identity of RPL27A (L27a) as a small basic protein of the 60S large ribosomal subunit, providing the foundational biochemical anchor for all later functional work.\",\n      \"evidence\": \"Protein sequencing of rat L27a from recombinant cDNA, N-terminal sequencing, Southern and Northern blot\",\n      \"pmids\": [\"2207170\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No human protein characterized directly\", \"No position within 60S architecture defined\", \"No functional or regulatory role addressed\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Defined the genomic and promoter architecture of human RPL27A, showing it has the TATA-less, Sp1/CpG-island regulatory features typical of ribosomal protein genes and mapping it to 11p15.\",\n      \"evidence\": \"Gene cloning, sequencing, FISH, and promoter analysis\",\n      \"pmids\": [\"10449908\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Transcriptional regulators not functionally validated\", \"No link from gene structure to protein function\", \"Splicing requirement (ATG separated by intron 1) not mechanistically tested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Placed RPL27A genetically upstream of p53 in ribosomal stress in vivo, showing that reduced RPL27A causes ataxia, pancytopenia, and hematopoietic defects that are p53-dependent.\",\n      \"evidence\": \"ENU mutagenesis sooty foot ataxia mouse, genetic epistasis with p53 heterozygosity, bone marrow/immunophenotyping\",\n      \"pmids\": [\"21674502\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism linking RPL27A loss to p53 activation not resolved\", \"Whether ribosome biogenesis defect is the trigger not directly shown\", \"c-Kit downregulation mechanism beyond p53-dependence undefined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Connected RPL27A loss to specific cellular outcomes—disrupted 60S biogenesis, nucleolar disintegration, protein-level p53 activation, apoptosis, and blocked erythroid differentiation—identifying it as a miR-595 target.\",\n      \"evidence\": \"miR-595 luciferase reporter, RPL27A knockdown/overexpression, ribosome subunit analysis, CD34+ differentiation assays\",\n      \"pmids\": [\"27374104\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical step from biogenesis defect to MDM2/p53 not mapped\", \"Erythroid specificity mechanism unexplained\", \"No reciprocal validation of the biogenesis vs. p53 ordering\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified a functional post-translational hydroxylation at His39 required for full ribosomal translational activity, giving the protein a role beyond passive structure.\",\n      \"evidence\": \"His39Ala/Thr and His40Ala mutagenesis with functional complementation and translation activity assay in HEK293 plus structural modeling\",\n      \"pmids\": [\"32492015\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Hydroxylating enzyme not identified\", \"No crystal structure or in vitro reconstitution\", \"Stoichiometry and regulation of hydroxylation unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Positioned Rpl27a within ATM-mediated DNA-damage signaling, showing radiation reduces Rpl27a and that this loss alters E2F1/p53 binding to MDM2.\",\n      \"evidence\": \"In vivo carbon-ion irradiation, proteomics/transcriptomics, GC-1 co-transfection, ATM inhibition, p53 knockout mice\",\n      \"pmids\": [\"32535367\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct physical interactions at MDM2 not demonstrated\", \"Mechanism by which RPL27A modulates MDM2 binding unclear\", \"Generality beyond spermatogonia untested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrated that His39 hydroxylation tunes selective mRNA translation, establishing RPL27A as a contributor to ribosome heterogeneity rather than a uniform structural component.\",\n      \"evidence\": \"His39Ala mutant transfection with polysome profiling and RNA-seq differential analysis in HEK293T\",\n      \"pmids\": [\"37047141\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Features determining mRNA selectivity not defined\", \"Physiological contexts where this matters unknown\", \"Link to specific cellular phenotypes not established\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined the post-translational stability control of RPL27A, showing K92/K94 ubiquitination drives degradation and that direct ligand binding at exons 4/5 stabilizes the protein and rescues impaired ribosome biogenesis.\",\n      \"evidence\": \"md-LED in vitro binding screen with martynoside, mutational mapping, ubiquitination proteomics, rRNA/ribosome assembly and nucleolar integrity assays\",\n      \"pmids\": [\"37481436\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Endogenous E3 ligase and deubiquitinase not identified\", \"Physiological ligand (if any) unknown\", \"Whether stabilization affects p53 axis not tested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Implicated RPL27A as a downstream mediator of an oncogenic tRNA fragment in breast cancer EMT and stemness phenotypes.\",\n      \"evidence\": \"Luciferase reporter, siRNA knockdown and rescue, migration/invasion/apoptosis and EMT marker assays\",\n      \"pmids\": [\"35030975\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct molecular mechanism for RPL27A's specific contribution established\", \"Reporter/knockdown correlative only\", \"Not independently validated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Associated RPL27A with cancer cell motility in triple-negative breast cancer in the context of EIF2 signaling.\",\n      \"evidence\": \"siRNA knockdown with migration/invasion assays and single-cell RNA-seq in MDA-MB-231\",\n      \"pmids\": [\"34497807\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No molecular mechanism for the motility phenotype\", \"EIF2 link correlative\", \"Knockdown effects may reflect general ribosome loss\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The enzyme that installs the His39 hydroxyl, the endogenous E3 ligase/DUB controlling K92/K94 ubiquitination, and the direct biochemical step connecting RPL27A loss to MDM2-p53 activation remain unidentified.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No hydroxylase identified\", \"No endogenous ubiquitination machinery defined\", \"Direct molecular link between ribosomal stress and MDM2/p53 not reconstituted\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [7, 0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [7, 0]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [2, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [2, 5]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"complexes\": [\"60S ribosomal large subunit\"],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}