{"gene":"RPL27","run_date":"2026-06-10T07:46:26","timeline":{"discoveries":[{"year":1998,"finding":"Deletion of the E. coli rpmA gene (encoding ribosomal protein L27) causes slow growth, cold- and temperature-sensitivity, accumulation of a 40S precursor to the 50S subunit deficient in proteins L16, L20, L21, and L27, and a 3-4-fold reduction in peptidyl transferase activity of 70S ribosomes. L27-lacking ribosomes are impaired in A-site tRNA binding (Phe-tRNAPhe) but not P-site binding, indicating L27 contributes to peptide bond formation by facilitating proper placement of the A-site tRNA acceptor end at the peptidyl transferase center.","method":"Gene deletion (rpmA knockout), ribosome assembly analysis by sedimentation, peptidyl transferase activity assay, tRNA binding assays (A-site and P-site)","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro enzymatic assays, genetic deletion with complementation, multiple orthogonal methods in a single rigorous study, replicated in subsequent work","pmids":["9677420"],"is_preprint":false},{"year":2005,"finding":"The N-terminal sequence of bacterial ribosomal protein L27 protrudes onto the interface of the 50S subunit and reaches the peptidyl transferase active site. Truncation of as few as 3 N-terminal amino acids reduces growth rate, impairs peptidyl transferase activity, and sharply decreases cross-linking of L27 to the 3' end of a photoreactive tRNA at the P site, demonstrating the flexible N-terminus is required for correct tRNA substrate positioning at the catalytic site.","method":"N-terminal truncation mutagenesis, growth rate assays, peptidyl transferase activity assays, photoreactive tRNA cross-linking at P site","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (mutagenesis + enzymatic assay + crosslinking), rigorous controls, consistent with independent structural data","pmids":["16285924"],"is_preprint":false},{"year":1987,"finding":"Immuno-electron microscopy using antibodies specific for E. coli L27 and reconstitution of 50S subunits from L27-lacking mutants with B. subtilis L27 localized ribosomal protein L27 at the base of the central protuberance on the interface side of the 50S particle, in proximity to the peptidyl transferase centre.","method":"Immuno-electron microscopy, 50S subunit reconstitution with heterologous L27","journal":"Molecular & general genetics : MGG","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two orthogonal localization approaches (antibody localization and reconstitution), single study","pmids":["3123891"],"is_preprint":false},{"year":1981,"finding":"RNA-protein cross-linking with 2-iminothiolane followed by UV irradiation in E. coli 50S subunits localized L27 cross-linking sites to positions 2332-2337 of 23S RNA, placing L27 in direct contact with the 23S rRNA near the peptidyl transferase region.","method":"RNA-protein cross-linking (2-iminothiolane + UV), RNA fragment analysis","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct cross-linking biochemistry, confirmed by a second independent cross-linking study (PMID 3278299)","pmids":["6170935","3278299"],"is_preprint":false},{"year":1988,"finding":"A second independent RNA-protein cross-linking study confirmed L27 contact with 23S RNA, refining the cross-link site to positions 2320-2323, further supporting L27 proximity to the peptidyl transferase center.","method":"RNA-protein cross-linking (2-iminothiolane + UV), affinity chromatography with antibodies, RNA fragment analysis","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — independent replication of cross-linking localization, two labs using same approach","pmids":["3278299"],"is_preprint":false},{"year":2004,"finding":"Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8 determined at 2.8 Å resolution by multiwavelength anomalous dispersion. The structure reveals an all-beta-sheet fold consisting of two sets of four-stranded beta-sheets around a hydrophobic core, with a highly positive surface charge consistent with RNA binding at the peptidyl transferase center.","method":"X-ray crystallography (MAD phasing), 2.8 Å resolution","journal":"Protein science : a publication of the Protein Society","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure at defined resolution, single lab but direct structural evidence","pmids":["15340170"],"is_preprint":false},{"year":2008,"finding":"Computer simulations of the peptidyl transfer reaction in T. thermophilus ribosomes predict that deletion of L27 causes only a minor reduction in the rate of peptide bond formation, consistent with the ribozyme view. The N-terminus of L27 is predicted to interact with the A76 phosphate group of A-site tRNA, explaining the observed impairment of A-site substrate binding in L27-lacking ribosomes. For puromycin (which lacks the A76 phosphate), deprotonation of the L27 N-terminal amine is predicted to accelerate the reaction, potentially explaining pH dependence differences.","method":"Molecular dynamics / free energy perturbation simulations of the PTC reaction","journal":"Biochemistry","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational prediction only, no direct experimental validation in this paper","pmids":["18393533"],"is_preprint":false},{"year":2012,"finding":"Single-molecule FRET measurements of tRNA dynamics at the peptidyl transfer center show that removing the first three N-terminal residues of L27 or mutating residue K4 reduces stable peptidyl tRNA formation after translocation, demonstrating that L27 stabilizes peptidyl tRNA at the P site and that K4 is a key residue for this stabilization.","method":"Single-molecule FRET (smFRET), L27 N-terminal truncation and point mutagenesis (K4)","journal":"Protein science : a publication of the Protein Society","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — smFRET with site-directed mutants, single lab, two orthogonal mutant constructs","pmids":["22930421"],"is_preprint":false},{"year":2015,"finding":"Fast kinetics experiments show that the rate of peptide-bond formation at physiological pH with aminoacyl-tRNA or puromycin is independent of the presence of L27; translation of natural mRNAs is only marginally affected in the absence of L27; and the pH dependence of the puromycin reaction is unaltered without L27, indicating the L27 N-terminal alpha-amine is not the ionizing group in catalysis. L27 is also not required for peptidyl-tRNA hydrolysis during termination. The primary functional role of L27 appears to be in subunit association rather than in the core mechanism of peptide bond formation.","method":"Rapid kinetics (stopped-flow), translation assays with natural mRNAs, pH-dependence measurements, L27 deletion strain","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal kinetic methods, rigorous in vitro reconstitution, directly tests and rejects earlier hypotheses","pmids":["26475831"],"is_preprint":false},{"year":2001,"finding":"A. aeolicus L27 expressed in an E. coli L27-deletion mutant is incorporated into completed E. coli ribosomes and can partially restore growth rate and ribosomal function, but unlike E. coli L27, fails to promote 50S subunit assembly, demonstrating a separable role for L27 in ribosome assembly versus translation.","method":"Heterologous complementation of L27 deletion mutant, growth rate assays, ribosome sedimentation analysis, CD and NMR spectroscopy","journal":"Journal of bacteriology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic complementation with heterologous protein, functional and structural separation of assembly vs. translation roles, single lab","pmids":["11673426"],"is_preprint":false},{"year":2014,"finding":"In Staphylococcus aureus and other Firmicutes, ribosomal protein L27 is encoded with an N-terminal extension absent from mature ribosomes. A conserved cysteine protease (Prp) performs post-translational N-terminal cleavage of L27. This processing is required for normal ribosomal function, as the extension is absent from mature ribosomes.","method":"Proteomics identification, biochemical characterization of Prp protease activity, sequence analysis of mature L27 vs precursor","journal":"Molecular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct identification of protease and cleavage event, biochemical characterization, single lab","pmids":["25388641"],"is_preprint":false},{"year":2025,"finding":"In S. pneumoniae, the Prp protease forms dimers that efficiently cleave ribosomal protein L27 in vitro at a specific N-terminal site. An inactive Prp variant (PrpC34S) binds L27 without cleaving it, and an L27 F12A mutation abolishes Prp binding, defining the cleavage site and protease-substrate interaction. Overexpression of PrpC34S in vivo is detrimental to S. pneumoniae growth. A Δprp strain is viable (unlike in S. aureus) because another protease can cleave L27, but a strain lacking the N-terminal extension shows impaired growth.","method":"In vitro cleavage assays, site-directed mutagenesis (PrpC34S, L27 F12A), in vivo overexpression, Δprp knockout, growth assays","journal":"bioRxiv : the preprint server for biology","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — in vitro reconstitution of cleavage, mutagenesis defining binding and cleavage sites, in vivo genetic data; preprint, not yet peer-reviewed","pmids":["40766419"],"is_preprint":true},{"year":2014,"finding":"Loss-of-function mutations in RPL27 (including a de novo splicing error mutation) cause Diamond-Blackfan anaemia. In vitro knockdown of RPL27 disturbs pre-ribosomal RNA processing. Zebrafish models of rpl27 mutation show impairments of erythrocyte production and developmental defects (tail and/or brain), establishing RPL27 as required for pre-rRNA processing and erythropoiesis.","method":"Whole-exome sequencing, in vitro siRNA knockdown with pre-rRNA processing analysis, zebrafish morpholino/mutant model with erythroid and developmental phenotype readouts","journal":"British journal of haematology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic identification plus functional validation in two systems (human cells and zebrafish), pre-rRNA processing directly measured","pmids":["25424902"],"is_preprint":false},{"year":2023,"finding":"siRNA-mediated silencing of RPL27 in human colorectal cancer cell lines (HCT116, HT29) suppresses cell proliferation, arrests cell cycle, and induces apoptosis in vitro and inhibits xenograft growth in vivo. RPL27 silencing downregulates PLK1 protein and G2/M regulators (phospho-CDC25C, CDK1, cyclin B1), and reduces sphere-forming capacity of CD133+ cancer stem cells with concurrent decreases in CD133 and PLK1, placing RPL27 upstream of PLK1 in a signaling axis controlling CRC proliferation and stemness.","method":"siRNA knockdown, CCK8/colony assays, FACS, xenograft mouse model, RNA sequencing, western blotting, sphere-forming assays","journal":"International journal of oncology","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — loss-of-function with multiple phenotypic readouts and pathway marker analysis, in vitro and in vivo, but pathway placement based on correlation of protein levels rather than direct epistasis","pmids":["37387446"],"is_preprint":false},{"year":1989,"finding":"Mouse ribosomal protein L27' (homolog of human RPL27) can functionally substitute for yeast ribosomal protein L29 in yeast ribosomes when yeast L29 is absent, supporting viability and normal growth. However, when both yeast L29 and mouse L27' are present, yeast L29 is preferentially assembled, demonstrating that the mammalian protein is structurally and functionally compatible with the eukaryotic ribosome core.","method":"Heterologous complementation in yeast (L29 deletion strain), cycloheximide resistance assay, growth assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic complementation with defined phenotypic rescue, single lab, demonstrates functional conservation of mammalian L27'","pmids":["2643099"],"is_preprint":false}],"current_model":"Human RPL27 is a component of the 60S ribosomal large subunit whose flexible N-terminus contacts the A- and P-site tRNAs near the peptidyl transferase center (PTC); it is required for pre-rRNA processing, 50S/60S subunit assembly, and A-site tRNA stabilization, but fast-kinetics experiments in the bacterial ortholog indicate it does not directly catalyze peptide bond formation (consistent with the ribosome-as-ribozyme model); loss-of-function mutations in human RPL27 cause Diamond-Blackfan anaemia by impairing pre-rRNA processing and erythropoiesis, and RPL27 knockdown in cancer cells suppresses proliferation through a PLK1-dependent pathway."},"narrative":{"mechanistic_narrative":"RPL27 is a conserved component of the large ribosomal subunit that sits at the base of the central protuberance on the interface side of the particle, in direct contact with 23S/large-subunit rRNA near the peptidyl transferase center (PTC) [PMID:3123891, PMID:6170935, PMID:3278299]. Its flexible N-terminus protrudes toward the catalytic site and positions the acceptor ends of tRNA substrates: truncation of the first few N-terminal residues impairs A-site tRNA placement and peptidyl transferase activity in the bacterial ortholog, and single-molecule measurements identify residue K4 as a key determinant of peptidyl-tRNA stabilization at the P site [PMID:16285924, PMID:22930421]. Despite this proximity to the active site, fast-kinetics analysis shows that peptide bond formation and peptidyl-tRNA hydrolysis proceed independently of L27, establishing that its primary contributions are to subunit association and substrate positioning rather than to catalysis itself, consistent with the ribosome-as-ribozyme model [PMID:26475831]. The role of L27 in assembly is genetically separable from its role in translation [PMID:11673426, PMID:9677420], and the mammalian protein is functionally interchangeable with the eukaryotic ribosomal core [PMID:2643099]. In humans, loss-of-function mutations in RPL27 cause Diamond-Blackfan anaemia by impairing pre-rRNA processing and erythropoiesis [PMID:25424902]. RPL27 silencing in colorectal cancer cells suppresses proliferation, arrests the cell cycle, and induces apoptosis through downregulation of PLK1 and G2/M regulators [PMID:37387446].","teleology":[{"year":1981,"claim":"Established the physical neighborhood of L27 within the large subunit by mapping it directly onto rRNA, the first step toward understanding where it acts.","evidence":"RNA-protein cross-linking (2-iminothiolane + UV) in E. coli 50S subunits, localizing L27 contacts to 23S rRNA positions 2332-2337","pmids":["6170935","3278299"],"confidence":"Medium","gaps":["Cross-link mapping gives proximity, not functional consequence","No structural model of the contact at this stage"]},{"year":1987,"claim":"Independently positioned L27 at the base of the central protuberance near the PTC, corroborating the rRNA cross-linking and locating it at the subunit interface.","evidence":"Immuno-electron microscopy and 50S reconstitution with heterologous B. subtilis L27","pmids":["3123891"],"confidence":"Medium","gaps":["Low resolution localization","Does not establish a catalytic or assembly role"]},{"year":1988,"claim":"Refined the rRNA cross-link site, reinforcing L27 proximity to the peptidyl transferase region.","evidence":"Independent RNA-protein cross-linking (2-iminothiolane + UV) with antibody affinity chromatography, refining the site to 23S positions 2320-2323","pmids":["3278299"],"confidence":"Medium","gaps":["Replication of localization but no functional assignment","Method-dependent site mapping"]},{"year":1989,"claim":"Showed the mammalian ortholog is functionally compatible with the eukaryotic ribosome, validating cross-kingdom inference about RPL27 function.","evidence":"Heterologous complementation of yeast L29 deletion by mouse L27', with cycloheximide-resistance and growth assays","pmids":["2643099"],"confidence":"Medium","gaps":["Functional substitution does not reveal mechanism","Yeast L29 is preferentially assembled when both present"]},{"year":1998,"claim":"Defined the functional consequences of losing L27, linking it to subunit assembly, peptidyl transferase activity, and specifically A-site tRNA binding.","evidence":"rpmA knockout in E. coli with sedimentation assembly analysis, peptidyl transferase assays, and A-/P-site tRNA binding assays","pmids":["9677420"],"confidence":"High","gaps":["Whether the PTC defect is direct catalysis or substrate positioning is unresolved","Assembly and translation roles not yet separated"]},{"year":2001,"claim":"Separated the assembly role of L27 from its translation role by showing a heterologous ortholog restores function but not assembly.","evidence":"Complementation of E. coli L27 deletion with A. aeolicus L27, sedimentation, CD and NMR spectroscopy","pmids":["11673426"],"confidence":"Medium","gaps":["Molecular basis of assembly defect not defined","Single heterologous protein tested"]},{"year":2004,"claim":"Provided an atomic-resolution fold for L27, revealing an all-beta architecture with a positively charged RNA-binding surface consistent with PTC contact.","evidence":"X-ray crystallography (MAD phasing) of T. thermophilus L27 at 2.8 Å","pmids":["15340170"],"confidence":"High","gaps":["Isolated protein structure, not in ribosome context","N-terminal flexible region not resolved functionally"]},{"year":2005,"claim":"Pinpointed the flexible N-terminus as the functional element reaching into the PTC and positioning tRNA substrate, refining the mechanism from 'L27 is near the PTC' to 'L27's N-terminus orients the tRNA acceptor end'.","evidence":"N-terminal truncation mutagenesis, growth and peptidyl transferase assays, photoreactive tRNA cross-linking at the P site","pmids":["16285924"],"confidence":"High","gaps":["Does not distinguish positioning from direct catalytic contribution","Residue-level determinants not yet mapped"]},{"year":2008,"claim":"Computationally predicted that L27 contributes to substrate binding (via the A76 phosphate of A-site tRNA) rather than catalysis, anticipating the ribozyme-consistent view.","evidence":"Molecular dynamics / free energy perturbation simulations of the PTC reaction in T. thermophilus","pmids":["18393533"],"confidence":"Low","gaps":["Computational prediction with no experimental validation in the study","Predicted puromycin pH effect untested here"]},{"year":2012,"claim":"Demonstrated at single-molecule resolution that L27 stabilizes peptidyl-tRNA at the P site and identified K4 as a key residue, assigning a specific dynamic role to the N-terminus.","evidence":"Single-molecule FRET of tRNA dynamics with L27 N-terminal truncation and K4 point mutants","pmids":["22930421"],"confidence":"Medium","gaps":["Single lab","Effect on overall translation rate not measured here"]},{"year":2015,"claim":"Resolved the long-standing catalysis question by showing peptide bond formation and termination hydrolysis are independent of L27, reassigning its primary role to subunit association and substrate positioning.","evidence":"Rapid stopped-flow kinetics, translation of natural mRNAs, pH-dependence measurements, and L27 deletion strain","pmids":["26475831"],"confidence":"High","gaps":["Mechanism of how L27 promotes subunit association not fully defined","Bacterial system; eukaryotic specifics not directly addressed"]},{"year":2014,"claim":"Connected RPL27 to human disease, showing loss-of-function causes Diamond-Blackfan anaemia via impaired pre-rRNA processing and erythropoiesis.","evidence":"Whole-exome sequencing, siRNA knockdown with pre-rRNA processing analysis, and zebrafish mutant/morphant models with erythroid and developmental readouts","pmids":["25424902"],"confidence":"High","gaps":["Tissue-selective sensitivity of erythropoiesis not mechanistically explained","Link between pre-rRNA processing defect and erythroid failure not detailed"]},{"year":2014,"claim":"Revealed that in some bacteria L27 requires post-translational N-terminal processing for function, identifying the Prp cysteine protease as the maturation enzyme.","evidence":"Proteomics, biochemical characterization of Prp protease activity, and sequence comparison of mature vs precursor L27 in S. aureus","pmids":["25388641"],"confidence":"Medium","gaps":["Relevance to eukaryotic RPL27 not established","Functional consequence of uncleaved extension not quantified"]},{"year":2023,"claim":"Placed RPL27 upstream of a PLK1-dependent proliferation and stemness axis in cancer, extending its role beyond housekeeping translation.","evidence":"siRNA knockdown in colorectal cancer lines with proliferation/cell-cycle/apoptosis assays, xenografts, RNA-seq, western blot of PLK1 and G2/M regulators, and sphere-forming assays","pmids":["37387446"],"confidence":"Medium","gaps":["Pathway placement based on protein-level correlation, not direct epistasis","Whether the effect is ribosome-dependent or extra-ribosomal is unresolved"]},{"year":2025,"claim":"Defined the Prp-L27 protease-substrate interaction at residue resolution and showed processing is required for optimal growth, while a redundant protease can substitute in some species.","evidence":"In vitro cleavage assays, PrpC34S and L27 F12A mutagenesis, in vivo overexpression and Δprp growth assays in S. pneumoniae (preprint)","pmids":["40766419"],"confidence":"Medium","gaps":["Preprint, not yet peer-reviewed","Identity of redundant protease not determined","No eukaryotic counterpart addressed"]},{"year":null,"claim":"How RPL27 mechanistically couples its ribosomal function to the PLK1 proliferation/stemness axis, and why erythroid progenitors are selectively vulnerable to RPL27 loss in humans, remain open.","evidence":"No direct mechanistic evidence in the available corpus connecting ribosomal function to the PLK1 axis or to erythroid-specific sensitivity","pmids":[],"confidence":"Low","gaps":["No direct epistasis linking RPL27 to PLK1","No mechanism for tissue-selective DBA phenotype","Extra-ribosomal functions of human RPL27 uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[3,4,5]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1,9]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[0,2,9]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[12]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,8]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[12]}],"complexes":["60S/50S large ribosomal subunit"],"partners":["PRP"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P61353","full_name":"Large ribosomal subunit protein eL27","aliases":["60S ribosomal protein L27"],"length_aa":136,"mass_kda":15.8,"function":"Component of the large ribosomal subunit (PubMed:12962325, PubMed:23636399, PubMed:25901680, PubMed:25957688, PubMed:32669547). Required for proper rRNA processing and maturation of 28S and 5.8S rRNAs (PubMed:25424902)","subcellular_location":"Cytoplasm, cytosol; Cytoplasm; Rough endoplasmic reticulum","url":"https://www.uniprot.org/uniprotkb/P61353/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPL27","classification":"Common Essential","n_dependent_lines":1208,"n_total_lines":1208,"dependency_fraction":1.0},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000131469","cell_line_id":"CID001902","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleolus_gc","grade":2}],"interactors":[{"gene":"ATG4B","stoichiometry":10.0},{"gene":"CAPRIN1","stoichiometry":10.0},{"gene":"DDX21","stoichiometry":10.0},{"gene":"DRG1","stoichiometry":10.0},{"gene":"EIF2S3","stoichiometry":10.0},{"gene":"ENY2","stoichiometry":10.0},{"gene":"G3BP1","stoichiometry":10.0},{"gene":"GSPT1","stoichiometry":10.0},{"gene":"METAP2","stoichiometry":10.0},{"gene":"NCAPH","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID001902","total_profiled":1310},"omim":[{"mim_id":"617409","title":"DIAMOND-BLACKFAN ANEMIA 17; DBA17","url":"https://www.omim.org/entry/617409"},{"mim_id":"617408","title":"DIAMOND-BLACKFAN ANEMIA 16; DBA16","url":"https://www.omim.org/entry/617408"},{"mim_id":"616717","title":"TESTIS-EXPRESSED GENE 10; TEX10","url":"https://www.omim.org/entry/616717"},{"mim_id":"607526","title":"RIBOSOMAL PROTEIN L27; RPL27","url":"https://www.omim.org/entry/607526"},{"mim_id":"604177","title":"RIBOSOMAL PROTEIN L8; RPL8","url":"https://www.omim.org/entry/604177"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoli","reliability":"Enhanced"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPL27"},"hgnc":{"alias_symbol":["L27","eL27"],"prev_symbol":[]},"alphafold":{"accession":"P61353","domains":[{"cath_id":"2.30.30.770","chopping":"8-130","consensus_level":"high","plddt":94.8668,"start":8,"end":130}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P61353","model_url":"https://alphafold.ebi.ac.uk/files/AF-P61353-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P61353-F1-predicted_aligned_error_v6.png","plddt_mean":94.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPL27","jax_strain_url":"https://www.jax.org/strain/search?query=RPL27"},"sequence":{"accession":"P61353","fasta_url":"https://rest.uniprot.org/uniprotkb/P61353.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P61353/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P61353"}},"corpus_meta":[{"pmid":"15504326","id":"PMC_15504326","title":"Quaternary structure, protein dynamics, and synaptic function of SAP97 controlled by L27 domain interactions.","date":"2004","source":"Neuron","url":"https://pubmed.ncbi.nlm.nih.gov/15504326","citation_count":206,"is_preprint":false},{"pmid":"25424902","id":"PMC_25424902","title":"Loss of function mutations in RPL27 and RPS27 identified by whole-exome sequencing in Diamond-Blackfan anaemia.","date":"2014","source":"British journal of haematology","url":"https://pubmed.ncbi.nlm.nih.gov/25424902","citation_count":84,"is_preprint":false},{"pmid":"16285924","id":"PMC_16285924","title":"A protein component at the heart of an RNA machine: the importance of protein l27 for the function of the bacterial ribosome.","date":"2005","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/16285924","citation_count":80,"is_preprint":false},{"pmid":"6170935","id":"PMC_6170935","title":"The use of 2-iminothiolane as an RNA-protein cross-linking agent in Escherichia coli ribosomes, and the localisation on 23S RNA of sites cross-linked to proteins L4, L6, L21, L23, L27 and L29.","date":"1981","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/6170935","citation_count":72,"is_preprint":false},{"pmid":"15048107","id":"PMC_15048107","title":"The tetrameric L27 domain complex as an organization platform for supramolecular assemblies.","date":"2004","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/15048107","citation_count":70,"is_preprint":false},{"pmid":"1002715","id":"PMC_1002715","title":"Isolation of eukaryotic ribosomal proteins. Purification and characterization of the 60 S ribosomal subunit proteins L4, L5, L7, L9, L11, L12, L13, L21, L22, L23, L26, L27, L30, L33, L35', L37, and L39.","date":"1976","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/1002715","citation_count":70,"is_preprint":false},{"pmid":"11724303","id":"PMC_11724303","title":"Enhanced expression of S8, L12, L23a, L27 and L30 ribosomal protein mRNAs in human hepatocellular carcinoma.","date":"2001","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/11724303","citation_count":69,"is_preprint":false},{"pmid":"863909","id":"PMC_863909","title":"Isolation of eukaryotic ribosomal proteins. Purification and characterization of 60 S ribosomal subunit proteins L3, L6, L7', L8, L10, L15, L17, L18, L19, L23', L25, L27', L28, L29, L31, L32, L34, L35, L36, L36', and L37'.","date":"1977","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/863909","citation_count":68,"is_preprint":false},{"pmid":"3278299","id":"PMC_3278299","title":"RNA-protein cross-linking in Escherichia coli 50S ribosomal subunits; determination of sites on 23S RNA that are cross-linked to proteins L2, L4, L24 and L27 by treatment with 2-iminothiolane.","date":"1988","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/3278299","citation_count":66,"is_preprint":false},{"pmid":"9677420","id":"PMC_9677420","title":"Ribosomal protein L27 participates in both 50 S subunit assembly and the peptidyl transferase reaction.","date":"1998","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9677420","citation_count":59,"is_preprint":false},{"pmid":"18393533","id":"PMC_18393533","title":"Role of ribosomal protein L27 in peptidyl transfer.","date":"2008","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18393533","citation_count":37,"is_preprint":false},{"pmid":"21059886","id":"PMC_21059886","title":"Central regulation of locomotor behavior of Drosophila melanogaster depends on a CASK isoform containing CaMK-like and L27 domains.","date":"2010","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/21059886","citation_count":35,"is_preprint":false},{"pmid":"15241471","id":"PMC_15241471","title":"Structural basis for L27 domain-mediated assembly of signaling and cell polarity complexes.","date":"2004","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/15241471","citation_count":34,"is_preprint":false},{"pmid":"29159916","id":"PMC_29159916","title":"Purification and characterization of ribosomal proteins L27 and L30 having antimicrobial activity produced by the Lactobacillus salivarius SGL 03.","date":"2018","source":"Journal of applied microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/29159916","citation_count":33,"is_preprint":false},{"pmid":"15863617","id":"PMC_15863617","title":"A unified assembly mode revealed by the structures of tetrameric L27 domain complexes formed by mLin-2/mLin-7 and Patj/Pals1 scaffold proteins.","date":"2005","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/15863617","citation_count":25,"is_preprint":false},{"pmid":"12110687","id":"PMC_12110687","title":"Coordinated folding and association of the LIN-2, -7 (L27) domain. An obligate heterodimerization involved in assembly of signaling and cell polarity complexes.","date":"2002","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12110687","citation_count":25,"is_preprint":false},{"pmid":"17913842","id":"PMC_17913842","title":"Lin-7 targets the Kir 2.3 channel on the basolateral membrane via a L27 domain interaction with CASK.","date":"2007","source":"American journal of physiology. Cell physiology","url":"https://pubmed.ncbi.nlm.nih.gov/17913842","citation_count":24,"is_preprint":false},{"pmid":"1709488","id":"PMC_1709488","title":"Ribosomal protein L27 is identical in chick and rat.","date":"1991","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/1709488","citation_count":22,"is_preprint":false},{"pmid":"378941","id":"PMC_378941","title":"Genes coding for ribosomal proteins S15, L21, and L27 map near argG in Escherichia coli.","date":"1979","source":"Journal of bacteriology","url":"https://pubmed.ncbi.nlm.nih.gov/378941","citation_count":22,"is_preprint":false},{"pmid":"25388641","id":"PMC_25388641","title":"Specific N-terminal cleavage of ribosomal protein L27 in Staphylococcus aureus and related bacteria.","date":"2014","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/25388641","citation_count":21,"is_preprint":false},{"pmid":"7804323","id":"PMC_7804323","title":"Phorbol ester induction of differentiation and apoptosis in the K562 cell line is accompanied by marked decreases in the stability of globin mRNAs and decreases in the steady state level of mRNAs encoding for ribosomal proteins L35, L31, L27, and L21.","date":"1994","source":"Cellular & molecular biology research","url":"https://pubmed.ncbi.nlm.nih.gov/7804323","citation_count":20,"is_preprint":false},{"pmid":"2643099","id":"PMC_2643099","title":"Functional substitution of mouse ribosomal protein L27' for yeast ribosomal protein L29 in yeast ribosomes.","date":"1989","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/2643099","citation_count":19,"is_preprint":false},{"pmid":"2833393","id":"PMC_2833393","title":"Nucleotide sequence of cloned cDNA specific for rat ribosomal protein L27.","date":"1988","source":"European journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/2833393","citation_count":17,"is_preprint":false},{"pmid":"6773542","id":"PMC_6773542","title":"Purification of Drosophila ribosomal proteins. Isolation of proteins S8, S13, S14, S16, S19, S20/L24, S22/L26, S24, S25/S27, S26, S29, L4, L10/L11, L12, L13, L16, L18, L19, L27, 1, 7/8, 9, and 11.","date":"1980","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/6773542","citation_count":16,"is_preprint":false},{"pmid":"22337881","id":"PMC_22337881","title":"Structure of an L27 domain heterotrimer from cell polarity complex Patj/Pals1/Mals2 reveals mutually independent L27 domain assembly mode.","date":"2012","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22337881","citation_count":15,"is_preprint":false},{"pmid":"12486522","id":"PMC_12486522","title":"Simultaneous horizontal gene transfer of a gene coding for ribosomal protein l27 and operational genes in Arthrobacter sp.","date":"2002","source":"Journal of molecular evolution","url":"https://pubmed.ncbi.nlm.nih.gov/12486522","citation_count":15,"is_preprint":false},{"pmid":"26475831","id":"PMC_26475831","title":"Activities of the peptidyl transferase center of ribosomes lacking protein L27.","date":"2015","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/26475831","citation_count":15,"is_preprint":false},{"pmid":"8148381","id":"PMC_8148381","title":"Cloning and nucleotide sequence of a full length cDNA encoding ribosomal protein L27 from human fetal kidney.","date":"1994","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/8148381","citation_count":14,"is_preprint":false},{"pmid":"37387446","id":"PMC_37387446","title":"RPL27 contributes to colorectal cancer proliferation and stemness via PLK1 signaling.","date":"2023","source":"International journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/37387446","citation_count":13,"is_preprint":false},{"pmid":"16603668","id":"PMC_16603668","title":"Promoter shuffling at a nuclear gene for mitochondrial RPL27. Involvement of interchromosome and subsequent intrachromosome recombinations.","date":"2006","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/16603668","citation_count":11,"is_preprint":false},{"pmid":"20702775","id":"PMC_20702775","title":"Structural basis for tandem L27 domain-mediated polymerization.","date":"2010","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/20702775","citation_count":10,"is_preprint":false},{"pmid":"8312607","id":"PMC_8312607","title":"Cloning and nucleotide sequencing of the genes, rpIU and rpmA, for ribosomal proteins L21 and L27 of Escherichia coli.","date":"1993","source":"DNA sequence : the journal of DNA sequencing and mapping","url":"https://pubmed.ncbi.nlm.nih.gov/8312607","citation_count":10,"is_preprint":false},{"pmid":"22930421","id":"PMC_22930421","title":"Role of the ribosomal protein L27 revealed by single-molecule FRET study.","date":"2012","source":"Protein science : a publication of the Protein Society","url":"https://pubmed.ncbi.nlm.nih.gov/22930421","citation_count":9,"is_preprint":false},{"pmid":"15340170","id":"PMC_15340170","title":"Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8.","date":"2004","source":"Protein science : a publication of the Protein Society","url":"https://pubmed.ncbi.nlm.nih.gov/15340170","citation_count":9,"is_preprint":false},{"pmid":"3123891","id":"PMC_3123891","title":"Localization of ribosomal protein L27 at the peptidyl transferase centre of the 50 S subunit, as determined by immuno-electron microscopy.","date":"1987","source":"Molecular & general genetics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/3123891","citation_count":8,"is_preprint":false},{"pmid":"2468568","id":"PMC_2468568","title":"Expression of naturally occurring RNA molecules complementary to the murine L27' ribosomal protein mRNA.","date":"1988","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/2468568","citation_count":7,"is_preprint":false},{"pmid":"32711152","id":"PMC_32711152","title":"Identification and characterization of SaRpAMP, a 60S ribosomal protein L27-derived antimicrobial peptide from amur catfish, Silurus asotus.","date":"2020","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/32711152","citation_count":6,"is_preprint":false},{"pmid":"29261291","id":"PMC_29261291","title":"Structures of the L27 Domain of Disc Large Homologue 1 Protein Illustrate a Self-Assembly Module.","date":"2018","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29261291","citation_count":6,"is_preprint":false},{"pmid":"27137500","id":"PMC_27137500","title":"Coexpression of Escherichia coli obgE, Encoding the Evolutionarily Conserved Obg GTPase, with Ribosomal Proteins L21 and L27.","date":"2016","source":"Journal of bacteriology","url":"https://pubmed.ncbi.nlm.nih.gov/27137500","citation_count":6,"is_preprint":false},{"pmid":"39622458","id":"PMC_39622458","title":"Identification of a novel antimicrobial peptide from amphioxus ribosomal protein L27.","date":"2024","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/39622458","citation_count":5,"is_preprint":false},{"pmid":"11673426","id":"PMC_11673426","title":"Differential effects of replacing Escherichia coli ribosomal protein L27 with its homologue from Aquifex aeolicus.","date":"2001","source":"Journal of bacteriology","url":"https://pubmed.ncbi.nlm.nih.gov/11673426","citation_count":5,"is_preprint":false},{"pmid":"25039062","id":"PMC_25039062","title":"Characterization and site-directed mutagenesis of a novel class II 5-enopyruvylshikimate-3-phosphate (EPSP) synthase from the deep-sea bacterium Alcanivorax sp. L27.","date":"2014","source":"Enzyme and microbial technology","url":"https://pubmed.ncbi.nlm.nih.gov/25039062","citation_count":5,"is_preprint":false},{"pmid":"12866796","id":"PMC_12866796","title":"Trypanosoma cruzi: identification and characterization of a novel ribosomal protein L27 (TcrL27) that cross-reacts with an affinity-purified anti-Sm antibody.","date":"2003","source":"Parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/12866796","citation_count":4,"is_preprint":false},{"pmid":"37812860","id":"PMC_37812860","title":"Effect of RPL27 knockdown on the proliferation and apoptosis of human liver cancer cells.","date":"2023","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/37812860","citation_count":3,"is_preprint":false},{"pmid":"39496834","id":"PMC_39496834","title":"The L27 domain of MPP7 enhances TAZ-YY1 cooperation to renew muscle stem cells.","date":"2024","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/39496834","citation_count":3,"is_preprint":false},{"pmid":"15501526","id":"PMC_15501526","title":"Ac His1 [D-Phe2, K15, R16, L27] VIP (3-7)/GRF (8-27)--a VPAC1 receptor antagonist--is an inverse agonist on two constitutively active truncated VPAC1 receptors.","date":"2004","source":"Peptides","url":"https://pubmed.ncbi.nlm.nih.gov/15501526","citation_count":3,"is_preprint":false},{"pmid":"39519211","id":"PMC_39519211","title":"Identification of Genes Associated with Familial Focal Segmental Glomerulosclerosis Through Transcriptomics and In Silico Analysis, Including RPL27, TUBB6, and PFDN5.","date":"2024","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/39519211","citation_count":1,"is_preprint":false},{"pmid":"22102253","id":"PMC_22102253","title":"Crystallization and preliminary X-ray data collection of the L27(PATJ)-(L27N,L27C)(Pals1)-L27(MALS) tripartite complex.","date":"2011","source":"Acta crystallographica. Section F, Structural biology and crystallization communications","url":"https://pubmed.ncbi.nlm.nih.gov/22102253","citation_count":1,"is_preprint":false},{"pmid":"8111025","id":"PMC_8111025","title":"The gene for ribosomal protein L27 is located on the plastid rather than the nuclear genome of the chlorophyll c-containing alga Pleurochrysis carterae.","date":"1994","source":"Plant molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8111025","citation_count":1,"is_preprint":false},{"pmid":"41004933","id":"PMC_41004933","title":"Ribosomal protein L27 contributes to virulence and maduramicin resistance in Eimeria tenella.","date":"2025","source":"International journal for parasitology. Drugs and drug resistance","url":"https://pubmed.ncbi.nlm.nih.gov/41004933","citation_count":0,"is_preprint":false},{"pmid":"38077061","id":"PMC_38077061","title":"The L27 Domain of MPP7 enhances TAZ-YY1 Cooperation to Renew Muscle Stem Cells.","date":"2023","source":"Research square","url":"https://pubmed.ncbi.nlm.nih.gov/38077061","citation_count":0,"is_preprint":false},{"pmid":"37961392","id":"PMC_37961392","title":"The L27 Domain of MPP7 enhances TAZ-YY1 Cooperation to Renew Muscle Stem Cells.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37961392","citation_count":0,"is_preprint":false},{"pmid":"38988374","id":"PMC_38988374","title":"De Novo Variant in the RPL27 Gene in a Second Infant with Diamond-Blackfan Anemia.","date":"2024","source":"Case reports in hematology","url":"https://pubmed.ncbi.nlm.nih.gov/38988374","citation_count":0,"is_preprint":false},{"pmid":"40766419","id":"PMC_40766419","title":"Cleavage of Streptococcus pneumoniae ribosomal protein L27 by the Prp protease.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40766419","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.01.668195","title":"Cleavage of  <i>Streptococcus pneumoniae</i>  ribosomal protein L27 by the Prp protease","date":"2025-08-01","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.01.668195","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":24764,"output_tokens":4510,"usd":0.070971,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11855,"output_tokens":4277,"usd":0.0831,"stage2_stop_reason":"end_turn"},"total_usd":0.154071,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"I need to carefully classify each paper before extracting. The query gene is RPL27 (human/mammalian ribosomal protein L27, also known as L27, eL27). I need to distinguish:\n\n1. **Human/mammalian RPL27** (the 60S large subunit ribosomal protein) - INCLUDE\n2. **Bacterial L27 homologs** (E. coli, T. thermophilus, S. aureus, S. pneumoniae) - these are orthologs in prokaryotic organisms; the mammalian RPL27 is the eukaryotic equivalent. These ARE orthologs relevant to understanding the protein's function in ribosome biology - INCLUDE as ortholog findings\n3. **L27 domain** (protein-protein interaction module in scaffold proteins like Lin-2/Lin-7, SAP97, CASK, Pals1, PATJ) - this is a DIFFERENT entity; the \"L27 domain\" is named after Lin-2/Lin-7 proteins, NOT after the ribosomal protein RPL27. These are about scaffold protein interaction domains, NOT the ribosomal protein RPL27 - EXCLUDE as alias collision\n4. **Plant/algal/parasite L27** - evaluate case by case\n\nPapers about the L27 protein-protein interaction domain (papers 1, 5, 12, 13, 15, 16, 17, 25, 31, 38, 45, 46, 51, 52) are about a DIFFERENT protein domain named after C. elegans Lin-2/Lin-7, not about the ribosomal protein RPL27. EXCLUDE.\n\nPaper 42 is about EPSPS from bacterium Alcanivorax sp. L27 - this is a strain name, not the gene. EXCLUDE.\n\nPaper 30 is about rice mitochondrial RPL27 - plant ortholog context but relevant to gene transfer biology, not mechanism of the human protein. The finding is about gene location/promoter, not mechanism. SKIP.\n\nNow extracting mechanistic findings about ribosomal protein L27 (RPL27):\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1998,\n      \"finding\": \"Deletion of the E. coli rpmA gene (encoding ribosomal protein L27) causes slow growth, cold- and temperature-sensitivity, accumulation of a 40S precursor to the 50S subunit deficient in proteins L16, L20, L21, and L27, and a 3-4-fold reduction in peptidyl transferase activity of 70S ribosomes. L27-lacking ribosomes are impaired in A-site tRNA binding (Phe-tRNAPhe) but not P-site binding, indicating L27 contributes to peptide bond formation by facilitating proper placement of the A-site tRNA acceptor end at the peptidyl transferase center.\",\n      \"method\": \"Gene deletion (rpmA knockout), ribosome assembly analysis by sedimentation, peptidyl transferase activity assay, tRNA binding assays (A-site and P-site)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro enzymatic assays, genetic deletion with complementation, multiple orthogonal methods in a single rigorous study, replicated in subsequent work\",\n      \"pmids\": [\"9677420\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"The N-terminal sequence of bacterial ribosomal protein L27 protrudes onto the interface of the 50S subunit and reaches the peptidyl transferase active site. Truncation of as few as 3 N-terminal amino acids reduces growth rate, impairs peptidyl transferase activity, and sharply decreases cross-linking of L27 to the 3' end of a photoreactive tRNA at the P site, demonstrating the flexible N-terminus is required for correct tRNA substrate positioning at the catalytic site.\",\n      \"method\": \"N-terminal truncation mutagenesis, growth rate assays, peptidyl transferase activity assays, photoreactive tRNA cross-linking at P site\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (mutagenesis + enzymatic assay + crosslinking), rigorous controls, consistent with independent structural data\",\n      \"pmids\": [\"16285924\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1987,\n      \"finding\": \"Immuno-electron microscopy using antibodies specific for E. coli L27 and reconstitution of 50S subunits from L27-lacking mutants with B. subtilis L27 localized ribosomal protein L27 at the base of the central protuberance on the interface side of the 50S particle, in proximity to the peptidyl transferase centre.\",\n      \"method\": \"Immuno-electron microscopy, 50S subunit reconstitution with heterologous L27\",\n      \"journal\": \"Molecular & general genetics : MGG\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two orthogonal localization approaches (antibody localization and reconstitution), single study\",\n      \"pmids\": [\"3123891\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1981,\n      \"finding\": \"RNA-protein cross-linking with 2-iminothiolane followed by UV irradiation in E. coli 50S subunits localized L27 cross-linking sites to positions 2332-2337 of 23S RNA, placing L27 in direct contact with the 23S rRNA near the peptidyl transferase region.\",\n      \"method\": \"RNA-protein cross-linking (2-iminothiolane + UV), RNA fragment analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct cross-linking biochemistry, confirmed by a second independent cross-linking study (PMID 3278299)\",\n      \"pmids\": [\"6170935\", \"3278299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1988,\n      \"finding\": \"A second independent RNA-protein cross-linking study confirmed L27 contact with 23S RNA, refining the cross-link site to positions 2320-2323, further supporting L27 proximity to the peptidyl transferase center.\",\n      \"method\": \"RNA-protein cross-linking (2-iminothiolane + UV), affinity chromatography with antibodies, RNA fragment analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — independent replication of cross-linking localization, two labs using same approach\",\n      \"pmids\": [\"3278299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8 determined at 2.8 Å resolution by multiwavelength anomalous dispersion. The structure reveals an all-beta-sheet fold consisting of two sets of four-stranded beta-sheets around a hydrophobic core, with a highly positive surface charge consistent with RNA binding at the peptidyl transferase center.\",\n      \"method\": \"X-ray crystallography (MAD phasing), 2.8 Å resolution\",\n      \"journal\": \"Protein science : a publication of the Protein Society\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure at defined resolution, single lab but direct structural evidence\",\n      \"pmids\": [\"15340170\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Computer simulations of the peptidyl transfer reaction in T. thermophilus ribosomes predict that deletion of L27 causes only a minor reduction in the rate of peptide bond formation, consistent with the ribozyme view. The N-terminus of L27 is predicted to interact with the A76 phosphate group of A-site tRNA, explaining the observed impairment of A-site substrate binding in L27-lacking ribosomes. For puromycin (which lacks the A76 phosphate), deprotonation of the L27 N-terminal amine is predicted to accelerate the reaction, potentially explaining pH dependence differences.\",\n      \"method\": \"Molecular dynamics / free energy perturbation simulations of the PTC reaction\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational prediction only, no direct experimental validation in this paper\",\n      \"pmids\": [\"18393533\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Single-molecule FRET measurements of tRNA dynamics at the peptidyl transfer center show that removing the first three N-terminal residues of L27 or mutating residue K4 reduces stable peptidyl tRNA formation after translocation, demonstrating that L27 stabilizes peptidyl tRNA at the P site and that K4 is a key residue for this stabilization.\",\n      \"method\": \"Single-molecule FRET (smFRET), L27 N-terminal truncation and point mutagenesis (K4)\",\n      \"journal\": \"Protein science : a publication of the Protein Society\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — smFRET with site-directed mutants, single lab, two orthogonal mutant constructs\",\n      \"pmids\": [\"22930421\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Fast kinetics experiments show that the rate of peptide-bond formation at physiological pH with aminoacyl-tRNA or puromycin is independent of the presence of L27; translation of natural mRNAs is only marginally affected in the absence of L27; and the pH dependence of the puromycin reaction is unaltered without L27, indicating the L27 N-terminal alpha-amine is not the ionizing group in catalysis. L27 is also not required for peptidyl-tRNA hydrolysis during termination. The primary functional role of L27 appears to be in subunit association rather than in the core mechanism of peptide bond formation.\",\n      \"method\": \"Rapid kinetics (stopped-flow), translation assays with natural mRNAs, pH-dependence measurements, L27 deletion strain\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal kinetic methods, rigorous in vitro reconstitution, directly tests and rejects earlier hypotheses\",\n      \"pmids\": [\"26475831\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"A. aeolicus L27 expressed in an E. coli L27-deletion mutant is incorporated into completed E. coli ribosomes and can partially restore growth rate and ribosomal function, but unlike E. coli L27, fails to promote 50S subunit assembly, demonstrating a separable role for L27 in ribosome assembly versus translation.\",\n      \"method\": \"Heterologous complementation of L27 deletion mutant, growth rate assays, ribosome sedimentation analysis, CD and NMR spectroscopy\",\n      \"journal\": \"Journal of bacteriology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic complementation with heterologous protein, functional and structural separation of assembly vs. translation roles, single lab\",\n      \"pmids\": [\"11673426\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In Staphylococcus aureus and other Firmicutes, ribosomal protein L27 is encoded with an N-terminal extension absent from mature ribosomes. A conserved cysteine protease (Prp) performs post-translational N-terminal cleavage of L27. This processing is required for normal ribosomal function, as the extension is absent from mature ribosomes.\",\n      \"method\": \"Proteomics identification, biochemical characterization of Prp protease activity, sequence analysis of mature L27 vs precursor\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct identification of protease and cleavage event, biochemical characterization, single lab\",\n      \"pmids\": [\"25388641\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In S. pneumoniae, the Prp protease forms dimers that efficiently cleave ribosomal protein L27 in vitro at a specific N-terminal site. An inactive Prp variant (PrpC34S) binds L27 without cleaving it, and an L27 F12A mutation abolishes Prp binding, defining the cleavage site and protease-substrate interaction. Overexpression of PrpC34S in vivo is detrimental to S. pneumoniae growth. A Δprp strain is viable (unlike in S. aureus) because another protease can cleave L27, but a strain lacking the N-terminal extension shows impaired growth.\",\n      \"method\": \"In vitro cleavage assays, site-directed mutagenesis (PrpC34S, L27 F12A), in vivo overexpression, Δprp knockout, growth assays\",\n      \"journal\": \"bioRxiv : the preprint server for biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro reconstitution of cleavage, mutagenesis defining binding and cleavage sites, in vivo genetic data; preprint, not yet peer-reviewed\",\n      \"pmids\": [\"40766419\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Loss-of-function mutations in RPL27 (including a de novo splicing error mutation) cause Diamond-Blackfan anaemia. In vitro knockdown of RPL27 disturbs pre-ribosomal RNA processing. Zebrafish models of rpl27 mutation show impairments of erythrocyte production and developmental defects (tail and/or brain), establishing RPL27 as required for pre-rRNA processing and erythropoiesis.\",\n      \"method\": \"Whole-exome sequencing, in vitro siRNA knockdown with pre-rRNA processing analysis, zebrafish morpholino/mutant model with erythroid and developmental phenotype readouts\",\n      \"journal\": \"British journal of haematology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic identification plus functional validation in two systems (human cells and zebrafish), pre-rRNA processing directly measured\",\n      \"pmids\": [\"25424902\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"siRNA-mediated silencing of RPL27 in human colorectal cancer cell lines (HCT116, HT29) suppresses cell proliferation, arrests cell cycle, and induces apoptosis in vitro and inhibits xenograft growth in vivo. RPL27 silencing downregulates PLK1 protein and G2/M regulators (phospho-CDC25C, CDK1, cyclin B1), and reduces sphere-forming capacity of CD133+ cancer stem cells with concurrent decreases in CD133 and PLK1, placing RPL27 upstream of PLK1 in a signaling axis controlling CRC proliferation and stemness.\",\n      \"method\": \"siRNA knockdown, CCK8/colony assays, FACS, xenograft mouse model, RNA sequencing, western blotting, sphere-forming assays\",\n      \"journal\": \"International journal of oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — loss-of-function with multiple phenotypic readouts and pathway marker analysis, in vitro and in vivo, but pathway placement based on correlation of protein levels rather than direct epistasis\",\n      \"pmids\": [\"37387446\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1989,\n      \"finding\": \"Mouse ribosomal protein L27' (homolog of human RPL27) can functionally substitute for yeast ribosomal protein L29 in yeast ribosomes when yeast L29 is absent, supporting viability and normal growth. However, when both yeast L29 and mouse L27' are present, yeast L29 is preferentially assembled, demonstrating that the mammalian protein is structurally and functionally compatible with the eukaryotic ribosome core.\",\n      \"method\": \"Heterologous complementation in yeast (L29 deletion strain), cycloheximide resistance assay, growth assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic complementation with defined phenotypic rescue, single lab, demonstrates functional conservation of mammalian L27'\",\n      \"pmids\": [\"2643099\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"Human RPL27 is a component of the 60S ribosomal large subunit whose flexible N-terminus contacts the A- and P-site tRNAs near the peptidyl transferase center (PTC); it is required for pre-rRNA processing, 50S/60S subunit assembly, and A-site tRNA stabilization, but fast-kinetics experiments in the bacterial ortholog indicate it does not directly catalyze peptide bond formation (consistent with the ribosome-as-ribozyme model); loss-of-function mutations in human RPL27 cause Diamond-Blackfan anaemia by impairing pre-rRNA processing and erythropoiesis, and RPL27 knockdown in cancer cells suppresses proliferation through a PLK1-dependent pathway.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPL27 is a conserved component of the large ribosomal subunit that sits at the base of the central protuberance on the interface side of the particle, in direct contact with 23S/large-subunit rRNA near the peptidyl transferase center (PTC) [#2, #3]. Its flexible N-terminus protrudes toward the catalytic site and positions the acceptor ends of tRNA substrates: truncation of the first few N-terminal residues impairs A-site tRNA placement and peptidyl transferase activity in the bacterial ortholog, and single-molecule measurements identify residue K4 as a key determinant of peptidyl-tRNA stabilization at the P site [#1, #7]. Despite this proximity to the active site, fast-kinetics analysis shows that peptide bond formation and peptidyl-tRNA hydrolysis proceed independently of L27, establishing that its primary contributions are to subunit association and substrate positioning rather than to catalysis itself, consistent with the ribosome-as-ribozyme model [#8]. The role of L27 in assembly is genetically separable from its role in translation [#9, #0], and the mammalian protein is functionally interchangeable with the eukaryotic ribosomal core [#14]. In humans, loss-of-function mutations in RPL27 cause Diamond-Blackfan anaemia by impairing pre-rRNA processing and erythropoiesis [#12]. RPL27 silencing in colorectal cancer cells suppresses proliferation, arrests the cell cycle, and induces apoptosis through downregulation of PLK1 and G2/M regulators [#13].\",\n  \"teleology\": [\n    {\n      \"year\": 1981,\n      \"claim\": \"Established the physical neighborhood of L27 within the large subunit by mapping it directly onto rRNA, the first step toward understanding where it acts.\",\n      \"evidence\": \"RNA-protein cross-linking (2-iminothiolane + UV) in E. coli 50S subunits, localizing L27 contacts to 23S rRNA positions 2332-2337\",\n      \"pmids\": [\"6170935\", \"3278299\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cross-link mapping gives proximity, not functional consequence\", \"No structural model of the contact at this stage\"]\n    },\n    {\n      \"year\": 1987,\n      \"claim\": \"Independently positioned L27 at the base of the central protuberance near the PTC, corroborating the rRNA cross-linking and locating it at the subunit interface.\",\n      \"evidence\": \"Immuno-electron microscopy and 50S reconstitution with heterologous B. subtilis L27\",\n      \"pmids\": [\"3123891\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Low resolution localization\", \"Does not establish a catalytic or assembly role\"]\n    },\n    {\n      \"year\": 1988,\n      \"claim\": \"Refined the rRNA cross-link site, reinforcing L27 proximity to the peptidyl transferase region.\",\n      \"evidence\": \"Independent RNA-protein cross-linking (2-iminothiolane + UV) with antibody affinity chromatography, refining the site to 23S positions 2320-2323\",\n      \"pmids\": [\"3278299\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Replication of localization but no functional assignment\", \"Method-dependent site mapping\"]\n    },\n    {\n      \"year\": 1989,\n      \"claim\": \"Showed the mammalian ortholog is functionally compatible with the eukaryotic ribosome, validating cross-kingdom inference about RPL27 function.\",\n      \"evidence\": \"Heterologous complementation of yeast L29 deletion by mouse L27', with cycloheximide-resistance and growth assays\",\n      \"pmids\": [\"2643099\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional substitution does not reveal mechanism\", \"Yeast L29 is preferentially assembled when both present\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Defined the functional consequences of losing L27, linking it to subunit assembly, peptidyl transferase activity, and specifically A-site tRNA binding.\",\n      \"evidence\": \"rpmA knockout in E. coli with sedimentation assembly analysis, peptidyl transferase assays, and A-/P-site tRNA binding assays\",\n      \"pmids\": [\"9677420\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the PTC defect is direct catalysis or substrate positioning is unresolved\", \"Assembly and translation roles not yet separated\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Separated the assembly role of L27 from its translation role by showing a heterologous ortholog restores function but not assembly.\",\n      \"evidence\": \"Complementation of E. coli L27 deletion with A. aeolicus L27, sedimentation, CD and NMR spectroscopy\",\n      \"pmids\": [\"11673426\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of assembly defect not defined\", \"Single heterologous protein tested\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Provided an atomic-resolution fold for L27, revealing an all-beta architecture with a positively charged RNA-binding surface consistent with PTC contact.\",\n      \"evidence\": \"X-ray crystallography (MAD phasing) of T. thermophilus L27 at 2.8 Å\",\n      \"pmids\": [\"15340170\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Isolated protein structure, not in ribosome context\", \"N-terminal flexible region not resolved functionally\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Pinpointed the flexible N-terminus as the functional element reaching into the PTC and positioning tRNA substrate, refining the mechanism from 'L27 is near the PTC' to 'L27's N-terminus orients the tRNA acceptor end'.\",\n      \"evidence\": \"N-terminal truncation mutagenesis, growth and peptidyl transferase assays, photoreactive tRNA cross-linking at the P site\",\n      \"pmids\": [\"16285924\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not distinguish positioning from direct catalytic contribution\", \"Residue-level determinants not yet mapped\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Computationally predicted that L27 contributes to substrate binding (via the A76 phosphate of A-site tRNA) rather than catalysis, anticipating the ribozyme-consistent view.\",\n      \"evidence\": \"Molecular dynamics / free energy perturbation simulations of the PTC reaction in T. thermophilus\",\n      \"pmids\": [\"18393533\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Computational prediction with no experimental validation in the study\", \"Predicted puromycin pH effect untested here\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrated at single-molecule resolution that L27 stabilizes peptidyl-tRNA at the P site and identified K4 as a key residue, assigning a specific dynamic role to the N-terminus.\",\n      \"evidence\": \"Single-molecule FRET of tRNA dynamics with L27 N-terminal truncation and K4 point mutants\",\n      \"pmids\": [\"22930421\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Effect on overall translation rate not measured here\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Resolved the long-standing catalysis question by showing peptide bond formation and termination hydrolysis are independent of L27, reassigning its primary role to subunit association and substrate positioning.\",\n      \"evidence\": \"Rapid stopped-flow kinetics, translation of natural mRNAs, pH-dependence measurements, and L27 deletion strain\",\n      \"pmids\": [\"26475831\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of how L27 promotes subunit association not fully defined\", \"Bacterial system; eukaryotic specifics not directly addressed\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Connected RPL27 to human disease, showing loss-of-function causes Diamond-Blackfan anaemia via impaired pre-rRNA processing and erythropoiesis.\",\n      \"evidence\": \"Whole-exome sequencing, siRNA knockdown with pre-rRNA processing analysis, and zebrafish mutant/morphant models with erythroid and developmental readouts\",\n      \"pmids\": [\"25424902\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Tissue-selective sensitivity of erythropoiesis not mechanistically explained\", \"Link between pre-rRNA processing defect and erythroid failure not detailed\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Revealed that in some bacteria L27 requires post-translational N-terminal processing for function, identifying the Prp cysteine protease as the maturation enzyme.\",\n      \"evidence\": \"Proteomics, biochemical characterization of Prp protease activity, and sequence comparison of mature vs precursor L27 in S. aureus\",\n      \"pmids\": [\"25388641\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relevance to eukaryotic RPL27 not established\", \"Functional consequence of uncleaved extension not quantified\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Placed RPL27 upstream of a PLK1-dependent proliferation and stemness axis in cancer, extending its role beyond housekeeping translation.\",\n      \"evidence\": \"siRNA knockdown in colorectal cancer lines with proliferation/cell-cycle/apoptosis assays, xenografts, RNA-seq, western blot of PLK1 and G2/M regulators, and sphere-forming assays\",\n      \"pmids\": [\"37387446\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Pathway placement based on protein-level correlation, not direct epistasis\", \"Whether the effect is ribosome-dependent or extra-ribosomal is unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined the Prp-L27 protease-substrate interaction at residue resolution and showed processing is required for optimal growth, while a redundant protease can substitute in some species.\",\n      \"evidence\": \"In vitro cleavage assays, PrpC34S and L27 F12A mutagenesis, in vivo overexpression and Δprp growth assays in S. pneumoniae (preprint)\",\n      \"pmids\": [\"40766419\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not yet peer-reviewed\", \"Identity of redundant protease not determined\", \"No eukaryotic counterpart addressed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RPL27 mechanistically couples its ribosomal function to the PLK1 proliferation/stemness axis, and why erythroid progenitors are selectively vulnerable to RPL27 loss in humans, remain open.\",\n      \"evidence\": \"No direct mechanistic evidence in the available corpus connecting ribosomal function to the PLK1 axis or to erythroid-specific sensitivity\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct epistasis linking RPL27 to PLK1\", \"No mechanism for tissue-selective DBA phenotype\", \"Extra-ribosomal functions of human RPL27 uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [3, 4, 5]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [0, 2, 9]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [12]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [12]}\n    ],\n    \"complexes\": [\n      \"60S/50S large ribosomal subunit\"\n    ],\n    \"partners\": [\n      \"Prp\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}