{"gene":"RPL36","run_date":"2026-06-10T07:46:26","timeline":{"discoveries":[{"year":1977,"finding":"RPL36 (L36) protein was isolated and purified from the 60S ribosomal large subunit of rat liver ribosomes, establishing it as a bona fide component of the eukaryotic large ribosomal subunit. Molecular weight and amino acid composition were determined.","method":"Ion exchange chromatography, gel filtration, SDS-PAGE, amino acid composition analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct biochemical isolation and characterization, replicated across multiple labs over decades","pmids":["863909"],"is_preprint":false},{"year":1993,"finding":"The primary amino acid sequence of rat RPL36 was determined: 104 amino acids (N-terminal Met cleaved post-translationally), MW ~12,128 Da, related to yeast ribosomal protein YL39. The mRNA is ~500 nt and there are 8–11 gene copies in the rat genome.","method":"cDNA sequencing, Southern blotting, Northern blotting","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct sequencing and structural determination with multiple orthogonal methods","pmids":["8484789"],"is_preprint":false},{"year":2000,"finding":"The solution NMR structure of ribosomal protein L36 from Thermus thermophilus revealed a zinc-ribbon-like fold: a triple-stranded antiparallel beta-sheet with a zinc-binding site (C-X2-C-X12-C-X4-H motif) coordinating zinc via three cysteines and one histidine (N-delta1). EXAFS confirmed equimolar zinc content. The electrostatic surface and conserved basic residues suggest a large L36-rRNA interaction interface. The fold topology resembles zinc-ribbon domains of transcription factors TFIIB and hTFIIS.","method":"Solution NMR structure determination, EXAFS spectroscopy, simulated annealing with NOE/dihedral restraints","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution NMR structure with orthogonal EXAFS validation of metal coordination","pmids":["10656825"],"is_preprint":false},{"year":2001,"finding":"The CCCH zinc-finger motif (C-X2-C-X12-C-X4-H) of Thermus thermophilus L36 binds metal ions with differential affinities in the order Co(II) > Hg(II) > Zn(II), as measured on a synthetic 26-mer peptide containing this motif.","method":"Solid-phase peptide synthesis, circular dichroism, capillary electrophoresis, electrospray ionization mass spectrometry, spectroscopic metal-binding assays","journal":"The journal of peptide research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro biochemical characterization on synthetic peptide, single lab, orthogonal spectroscopic methods but isolated peptide not full protein","pmids":["11168885"],"is_preprint":false},{"year":2005,"finding":"Metal-binding affinities of L36 zinc-ribbon protein are modulated by mutations in the beta-sheet hydrophobic cluster and beta-hairpin turn without changing the overall fold. Specifically: His32→Cys decreases affinity for both Zn(II) and Co(II); Tyr24→Trp increases both affinities; His20→Asn also increases both affinities. The protein normally binds Zn(II) ~2800-fold more tightly than Co(II).","method":"UV-vis spectroscopy metal-binding assays, circular dichroism, size-exclusion chromatography, 1D and 2D 1H NMR, site-directed mutagenesis","journal":"Journal of biological inorganic chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro mutagenesis with multiple orthogonal biophysical methods, single lab","pmids":["15747135"],"is_preprint":false},{"year":2006,"finding":"Functional cloning demonstrated that transfection of RPL36 cDNA conferred 2.5- to 3-fold cisplatin resistance in KB-3-1 cells, identifying RPL36 as a gene directly contributing to cisplatin resistance (confirmed in two independent transfection experiments).","method":"Retroviral cDNA library functional cloning, cisplatin selection, clonogenic assays, cDNA transfection","journal":"Molecular pharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional gain-of-function cloning with defined phenotypic readout, replicated in two independent transfection experiments, single lab","pmids":["16394183"],"is_preprint":false},{"year":2014,"finding":"In Saccharomyces cerevisiae, RPL36A/B (encoding L36a/b) is required for processing of 27SA2, 27SA3, and 27SBL pre-rRNAs during 60S ribosomal subunit biogenesis. RPL36A/B overexpression suppresses ebp2 mutant growth defects. Two-hybrid analysis showed L36a/b physically interacts with the assembly factor Ebp2, as well as ribosomal proteins L34a/b and L8 (which are adjacent to the 3′ end of 5.8S rRNA in mature ribosomes).","method":"Genetic suppression analysis (multicopy suppressor screen), synthetic growth enhancement, primer-extension pre-rRNA processing analysis, yeast two-hybrid","journal":"Current genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple genetic and molecular methods (suppressor screen, pre-rRNA processing, two-hybrid) in single lab, yeast ortholog","pmids":["25119672"],"is_preprint":false},{"year":2014,"finding":"In a zebrafish pancreatic cancer model, rpl36 heterozygous loss (haploinsufficiency) accelerated KRAS(G12V)-driven tumor progression and decreased survival in pancreatic acinar cells, establishing rpl36 as a haploinsufficient tumor suppressor in this context. rpl23a did not show this effect, indicating specificity.","method":"Zebrafish genetic model (rpl36 hi1807/+ heterozygous mutants crossed with ptf1a:gal4VP16;UAS:GFP-KRAS(G12V) transgenic fish), survival analysis, genetic epistasis","journal":"Zebrafish","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo genetic loss-of-function with defined oncogenic context and survival endpoint, zebrafish ortholog, single lab","pmids":["25380065"],"is_preprint":false},{"year":2016,"finding":"Ribosomal protein eL36 (RPL36) modulates translation of Hsp90α mRNA. Elevated eL36 (and eL42) levels in rhabdomyosarcoma drive high Hsp90 expression and modulate sensitivity to the Hsp90 inhibitor 17-AAG. Polysome profiling showed Hsp90α mRNA is selectively translated under heat stress conditions where global translation is inhibited.","method":"Polysome profiling, RNA interference/knockdown, Hsp90 inhibitor sensitivity assay (17-AAG), rhabdomyosarcoma cell lines","journal":"Translation (Austin, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — polysome profiling with functional inhibitor sensitivity readout, single lab, two orthogonal methods","pmids":["28090422"],"is_preprint":false},{"year":2017,"finding":"In glioma cells, RPL36 promotes cell proliferation and G1/S cell cycle progression. STAT1 was identified by mass spectrometry as a protein that interacts with both lncRNA PLAC2 and the RPL36 promoter, binding at the RPL36 promoter to regulate its expression. Nuclear PLAC2 binds STAT1 and interacts with the RPL36 promoter, while cytoplasmic PLAC2 inhibits STAT1 nuclear translocation, thereby decreasing RPL36 expression and inducing cell cycle arrest.","method":"Mass spectrometry (co-immunoprecipitation-MS), cell proliferation assays, cell cycle analysis (flow cytometry), nuclear/cytoplasmic fractionation, ChIP/promoter binding assays, siRNA knockdown","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mass spectrometry identification of STAT1 interaction, cell cycle functional readout, multiple methods, single lab","pmids":["28922548"],"is_preprint":false},{"year":2020,"finding":"In zinc-deficient E. coli, the zinc-binding ribosomal protein L36 (encoded by rpmJ) is replaced at its ribosomal binding site by the paralog YkgO (expressed from the ykgM operon under Zur repressor control). Copy numbers of L36 and YkgO sum to 1, indicating they share a single binding site. Loss of rpmJ impairs late assembly of the 50S particle, reduces in vitro translation, and causes growth defects; YkgO rescues these functions in zur mutant cells.","method":"Genetic deletion (rpmJ null mutants), suppressor mutant isolation (zur mutations), ribosome fractionation, in vitro translation assays, copy number quantitation","journal":"Genes to cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and biochemical analysis with defined functional readouts in E. coli, multiple orthogonal methods, single lab","pmids":["32559334"],"is_preprint":false},{"year":2021,"finding":"Alt-RPL36, a protein co-encoded with human RPL36 from an alternative ORF in the same transcript, partially localizes to the endoplasmic reticulum and interacts with TMEM24 (a PI transfer protein). Knockout of alt-RPL36 increases plasma membrane PI(4,5)P2 levels, upregulates PI3K-AKT-mTOR signaling, and increases cell size. Alt-RPL36 contains four phosphoserine residues; point mutations abolishing these phosphorylations eliminate TMEM24 interaction and consequently ablate alt-RPL36 effects on PI3K signaling and cell size.","method":"Alternative ORF detection, co-immunoprecipitation, knockout (CRISPR), PI(4,5)P2 biosensor imaging, PI3K-AKT-mTOR signaling assays (phospho-Western), cell size measurement, phosphosite mutagenesis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (Co-IP, KO, PI biosensor, mutagenesis, signaling assays) in a single rigorous study","pmids":["33479206"],"is_preprint":false},{"year":2021,"finding":"Knockdown of RpL36 in Drosophila melanogaster testes impairs spermatogenesis: causes smaller testes, reduced germ cells (including germ stem cells), enlarged hub cell clusters, fewer mature sperm, increased apoptosis (TUNEL signal in non-germ cells), and reduced pH3-positive (mitotic) germ cells. Transcriptome analysis of knockdown testes showed altered expression of genes in cell death, cell cycle progression, and JAK/STAT signaling pathway.","method":"RNAi knockdown (testis-specific), immunofluorescence (Vasa, pH3), TUNEL assay, fertility assay (egg hatch rate), gene expression analysis","journal":"Journal of experimental zoology. Part B, Molecular and developmental evolution","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo loss-of-function with multiple cellular phenotype readouts, Drosophila ortholog, single lab","pmids":["33734578"],"is_preprint":false},{"year":2023,"finding":"In Saccharomyces cerevisiae, depletion of eL36 not only blocks its own assembly into pre-60S particles but also impairs assembly of neighboring ribosomal proteins eL15 and eL8 into early pre-60S particles, and causes loss of most A3- and B-factors (assembly factors for 27SA3 and 27SB pre-rRNA processing). These results indicate that eL36, together with eL8 and eL15, is prerequisite for shaping domain I of 5.8S/25S rRNA within early pre-60S particles.","method":"Conditional depletion (in vivo), pre-rRNA processing analysis, mass spectrometry analysis of pre-60S particle composition, genetic/biochemical epistasis","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo depletion with MS-based particle composition analysis and pre-rRNA processing, yeast ortholog, single lab","pmids":["37865285"],"is_preprint":false},{"year":2024,"finding":"m6A modification of RPL36 mRNA reduces its stability and thereby decreases RPL36 expression. The m6A reader IGF2BP1 directly binds RPL36 mRNA to attenuate this destabilization, maintaining RPL36 expression and cell proliferation. In benzene-exposed cells/animals, reduced IGF2BP1 leads to hypomethylation and reduced RPL36 expression, impairing cell proliferation; IGF2BP1 overexpression rescues RPL36 mRNA levels and proliferation.","method":"m6A transcriptome-wide sequencing (MeRIP-seq), RNA stability assays, IGF2BP1 overexpression (in vitro and in vivo mouse model), mRNA expression analysis, cell proliferation assays","journal":"Toxicology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — transcriptome-wide m6A mapping combined with in vitro and in vivo functional rescue, single lab, multiple orthogonal methods","pmids":["38367942"],"is_preprint":false},{"year":2025,"finding":"RPL36 functions as an RNA-binding protein and sorting regulator of microRNA-4432 into extracellular vesicles in TIE2(L914F)-mutant endothelial cells (venous malformation model). RPL36-mediated selective loading of miR-4432 into EVs contributes to inhibition of perivascular cell differentiation, adhesion, and proliferation, identified by miRNA pulldown and RNA interference.","method":"RNA sequencing (miRNA profiling of cells and EVs), miRNA pulldown, RNA interference, functional assays (differentiation, adhesion, proliferation of umbilical cord stem cells)","journal":"The British journal of dermatology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — miRNA pulldown plus RNAi with defined functional readouts, single lab, multiple orthogonal methods","pmids":["39700429"],"is_preprint":false}],"current_model":"RPL36 is a zinc-ribbon domain-containing component of the 60S ribosomal large subunit that binds rRNA via conserved basic residues, is required for pre-rRNA processing (27SA2/27SA3/27SB) and late 50S/60S assembly cooperatively with neighboring ribosomal proteins eL8 and eL15, promotes G1/S cell cycle progression and cell proliferation, confers cisplatin resistance, and acts as a haploinsufficient tumor suppressor in the context of oncogenic KRAS; additionally, RPL36 selectively modulates translation of Hsp90α mRNA, functions as an RNA-binding protein that sorts miR-4432 into extracellular vesicles, and its mRNA stability is regulated by m6A modification read by IGF2BP1, while a co-encoded alternative ORF (alt-RPL36) independently regulates PI3K-AKT-mTOR signaling through phosphoserine-dependent interaction with the PI transfer protein TMEM24 at the endoplasmic reticulum."},"narrative":{"mechanistic_narrative":"RPL36 (eL36) is a zinc-ribbon-domain protein component of the eukaryotic 60S large ribosomal subunit, originally isolated as a ~12 kDa basic protein from rat liver ribosomes [PMID:863909, PMID:8484789]. Structural work on the bacterial counterpart established its defining fold: a triple-stranded antiparallel beta-sheet stabilized by a CCCH zinc-binding motif (C-X2-C-X12-C-X4-H) whose conserved basic surface forms an extensive rRNA-interaction interface [PMID:10656825]. During subunit biogenesis, eL36 is required for processing of 27SA2, 27SA3, and 27SB pre-rRNAs and acts cooperatively with the neighboring ribosomal proteins eL8 and eL15 to shape domain I of 5.8S/25S rRNA in early pre-60S particles, with its depletion also blocking recruitment of A3- and B-class assembly factors [PMID:25119672, PMID:37865285]. Beyond its core ribosomal role, RPL36 promotes cell proliferation and G1/S cell cycle progression, a function controlled at the promoter by STAT1 [PMID:28922548], and its mRNA stability is set by m6A modification read by IGF2BP1 [PMID:38367942]. RPL36 contributes to cisplatin resistance [PMID:16394183] and behaves as a haploinsufficient tumor suppressor that accelerates KRAS-driven pancreatic tumorigenesis when lost [PMID:25380065]. It also exhibits extra-ribosomal activities, selectively modulating Hsp90α mRNA translation [PMID:28090422] and acting as an RNA-binding protein that sorts miR-4432 into extracellular vesicles [PMID:39700429]. Notably, an alternative ORF in the same transcript encodes alt-RPL36, a distinct ER-associated protein that, through phosphoserine-dependent binding to the PI transfer protein TMEM24, restrains plasma-membrane PI(4,5)P2 levels and PI3K-AKT-mTOR signaling [PMID:33479206].","teleology":[{"year":1977,"claim":"Established RPL36 as a genuine constituent of the eukaryotic large ribosomal subunit rather than a contaminant, defining the physical object all later work concerns.","evidence":"Biochemical purification from rat liver 60S subunits with SDS-PAGE and amino acid composition analysis","pmids":["863909"],"confidence":"High","gaps":["No sequence or structural information at this stage","Functional role within the ribosome undefined"]},{"year":1993,"claim":"Provided the primary sequence and gene-copy context, anchoring RPL36 to the conserved YL39 ribosomal protein family and enabling molecular study.","evidence":"cDNA sequencing with Southern and Northern blotting in rat","pmids":["8484789"],"confidence":"High","gaps":["No three-dimensional structure","rRNA contacts not mapped"]},{"year":2000,"claim":"Resolved the fold as a zinc-ribbon with a CCCH zinc-coordination site and a basic rRNA-binding surface, explaining how the protein engages rRNA.","evidence":"Solution NMR structure and EXAFS metal validation of Thermus thermophilus L36","pmids":["10656825"],"confidence":"High","gaps":["Structure from bacterial ortholog, not human protein","rRNA interface inferred from electrostatics, not co-structure"]},{"year":2005,"claim":"Defined the determinants of metal selectivity in the zinc-ribbon, showing the fold strongly favors Zn(II) and that specific residues tune affinity without disrupting topology.","evidence":"Site-directed mutagenesis with UV-vis, CD, and NMR metal-binding assays on the bacterial protein (extends 2001 peptide work)","pmids":["15747135","11168885"],"confidence":"Medium","gaps":["In vitro biophysics on bacterial protein/peptide","Physiological relevance of metal selectivity in the assembled ribosome untested"]},{"year":2014,"claim":"Placed RPL36 in the 60S biogenesis pathway by showing it is needed for specific pre-rRNA processing steps and physically links to assembly factor Ebp2 and neighboring r-proteins.","evidence":"Multicopy suppressor screen, primer-extension pre-rRNA analysis, and yeast two-hybrid in S. cerevisiae","pmids":["25119672"],"confidence":"Medium","gaps":["Interaction order and direct vs. indirect contacts not resolved","Yeast ortholog; human pathway not directly tested"]},{"year":2014,"claim":"Demonstrated a context-specific tumor-suppressor role, with haploinsufficient rpl36 loss accelerating oncogenic KRAS-driven cancer, distinguishing it from a generic ribosomal protein.","evidence":"Zebrafish heterozygous mutant crossed to KRAS(G12V) pancreatic model with survival analysis","pmids":["25380065"],"confidence":"Medium","gaps":["Mechanism linking reduced RPL36 to tumor acceleration unknown","Specificity to KRAS context not generalized"]},{"year":2016,"claim":"Identified an extra-ribosomal translational specialization, with RPL36 levels selectively modulating Hsp90α mRNA translation and chaperone-inhibitor sensitivity.","evidence":"Polysome profiling and Hsp90 inhibitor sensitivity assays after knockdown in rhabdomyosarcoma cells","pmids":["28090422"],"confidence":"Medium","gaps":["Mechanism of mRNA selectivity not defined","Whether effect requires intact ribosome vs. free RPL36 unclear"]},{"year":2017,"claim":"Connected RPL36 expression to proliferation control via an upstream STAT1/lncRNA regulatory axis acting at the RPL36 promoter.","evidence":"Co-IP-MS, ChIP/promoter binding, fractionation, and cell-cycle assays in glioma cells","pmids":["28922548"],"confidence":"Medium","gaps":["Direct vs. indirect STAT1 promoter occupancy not fully separated","Downstream proliferation effectors of RPL36 not identified"]},{"year":2020,"claim":"Confirmed the conserved structural-zinc and late-assembly role through bacterial paralog substitution, showing L36 occupies a single binding site essential for 50S maturation.","evidence":"rpmJ deletion, ykgM/YkgO paralog rescue, ribosome fractionation, and in vitro translation in E. coli","pmids":["32559334"],"confidence":"Medium","gaps":["Bacterial system; eukaryotic zinc-homeostasis link untested","Whether human RPL36 has an analogous paralog switch unknown"]},{"year":2021,"claim":"Revealed a dual-coding transcript in which an alternative ORF (alt-RPL36) acts independently of ribosome biogenesis to restrain PI3K-AKT-mTOR signaling via phosphoserine-dependent TMEM24 binding at the ER.","evidence":"Alt-ORF detection, Co-IP, CRISPR knockout, PI(4,5)P2 biosensor imaging, phosphosite mutagenesis, and signaling assays","pmids":["33479206"],"confidence":"High","gaps":["Kinase phosphorylating alt-RPL36 not identified","Relationship between canonical RPL36 and alt-RPL36 functions not integrated"]},{"year":2021,"claim":"Showed RPL36 is required in vivo for tissue homeostasis, with knockdown disrupting spermatogenesis through altered cell death, cell cycle, and JAK/STAT gene expression.","evidence":"Testis-specific RNAi, immunofluorescence, TUNEL, and transcriptome analysis in Drosophila","pmids":["33734578"],"confidence":"Medium","gaps":["Phenotype may reflect general ribosome insufficiency","Direct targets of RPL36 in germline not defined"]},{"year":2024,"claim":"Defined post-transcriptional control of RPL36 abundance, showing m6A destabilizes its mRNA while the reader IGF2BP1 protects the transcript to sustain proliferation.","evidence":"MeRIP-seq, RNA stability assays, and IGF2BP1 gain-of-function rescue in vitro and in benzene-exposed mice","pmids":["38367942"],"confidence":"Medium","gaps":["Writer/eraser enzymes setting the m6A mark not identified","Whether proliferation effect is ribosomal or extra-ribosomal unresolved"]},{"year":2025,"claim":"Extended RPL36's RNA-binding repertoire to selective miRNA cargo sorting, loading miR-4432 into extracellular vesicles to influence perivascular cell behavior.","evidence":"miRNA pulldown, RNAi, and functional differentiation/adhesion/proliferation assays in TIE2-mutant endothelial cells","pmids":["39700429"],"confidence":"Medium","gaps":["RNA-binding determinants of RPL36 for miR-4432 not mapped","Generality of EV-sorting function beyond venous malformation context unknown"]},{"year":null,"claim":"How RPL36's canonical ribosomal role mechanistically connects to its extra-ribosomal activities (selective translation, EV miRNA sorting, tumor suppression) and to the independently acting alt-RPL36 remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of human RPL36 within the 60S subunit in the corpus","Mechanism partitioning free vs. ribosome-bound RPL36 functions undefined","Causal link between RPL36 dosage and KRAS-context tumor suppression unexplained"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[8,15]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,2,13]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[8]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[11]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[6,13]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,8]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[9]}],"complexes":["60S large ribosomal subunit"],"partners":["EL8","EL15","EBP2","TMEM24","STAT1","IGF2BP1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"C0HME6","full_name":"RPL36 alternative reading frame protein","aliases":[],"length_aa":148,"mass_kda":15.8,"function":"Inhibits C2CD2L/TMEM24-dependent transport of phosphatidylinositol, the precursor of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), from its site of synthesis in the endoplasmic reticulum to the cell membrane (PubMed:33479206). This leads to down-regulation of the PI3K-AKT-mTOR signaling pathway (PubMed:33479206)","subcellular_location":"Endoplasmic reticulum","url":"https://www.uniprot.org/uniprotkb/C0HME6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPL36","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":"CTCF","stoichiometry":10.0},{"gene":"EIF2S3","stoichiometry":10.0},{"gene":"NUCKS1","stoichiometry":10.0},{"gene":"RPL11","stoichiometry":10.0},{"gene":"RPL19","stoichiometry":10.0},{"gene":"RPL4","stoichiometry":10.0},{"gene":"RPL5","stoichiometry":10.0},{"gene":"RPS16","stoichiometry":10.0},{"gene":"SEC61B","stoichiometry":10.0},{"gene":"SRP68","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/RPL36","total_profiled":1310},"omim":[{"mim_id":"617893","title":"RIBOSOMAL PROTEIN L36; RPL36","url":"https://www.omim.org/entry/617893"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPL36"},"hgnc":{"alias_symbol":["DKFZp566B023","L36","eL36"],"prev_symbol":[]},"alphafold":{"accession":"C0HME6","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/C0HME6","model_url":"","pae_url":"","plddt_mean":null},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPL36","jax_strain_url":"https://www.jax.org/strain/search?query=RPL36"},"sequence":{"accession":"C0HME6","fasta_url":"https://rest.uniprot.org/uniprotkb/C0HME6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/C0HME6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/C0HME6"}},"corpus_meta":[{"pmid":"28922548","id":"PMC_28922548","title":"LncRNA PLAC2 down-regulates RPL36 expression and blocks cell cycle progression in glioma through a mechanism involving STAT1.","date":"2017","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/28922548","citation_count":87,"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":"33479206","id":"PMC_33479206","title":"Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33479206","citation_count":47,"is_preprint":false},{"pmid":"10656825","id":"PMC_10656825","title":"The solution structure of ribosomal protein L36 from Thermus thermophilus reveals a zinc-ribbon-like fold.","date":"2000","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10656825","citation_count":42,"is_preprint":false},{"pmid":"19230943","id":"PMC_19230943","title":"Aromatase inhibitory, radical scavenging, and antioxidant activities of depsidones and diaryl ethers from the endophytic fungus Corynespora cassiicola L36.","date":"2009","source":"Phytochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19230943","citation_count":41,"is_preprint":false},{"pmid":"16394183","id":"PMC_16394183","title":"Identification by functional cloning from a retroviral cDNA library of cDNAs for ribosomal protein L36 and the 10-kDa heat shock protein that confer cisplatin resistance.","date":"2006","source":"Molecular pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/16394183","citation_count":30,"is_preprint":false},{"pmid":"7621528","id":"PMC_7621528","title":"Rat intestinal galactoside-binding lectin L-36 functions as a structural protein in the superficial squamous cells of the esophageal epithelium.","date":"1995","source":"Cell and tissue research","url":"https://pubmed.ncbi.nlm.nih.gov/7621528","citation_count":26,"is_preprint":false},{"pmid":"25380065","id":"PMC_25380065","title":"The tumor suppressor rpl36 restrains KRAS(G12V)-induced pancreatic cancer.","date":"2014","source":"Zebrafish","url":"https://pubmed.ncbi.nlm.nih.gov/25380065","citation_count":21,"is_preprint":false},{"pmid":"16116291","id":"PMC_16116291","title":"Disruption of rpmJ encoding ribosomal protein L36 decreases the expression of secY upstream of the spc operon and inhibits protein translocation in Escherichia coli.","date":"2005","source":"Bioscience, biotechnology, and biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16116291","citation_count":21,"is_preprint":false},{"pmid":"32559334","id":"PMC_32559334","title":"YkgM and YkgO maintain translation by replacing their paralogs, zinc-binding ribosomal proteins L31 and L36, with identical activities.","date":"2020","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/32559334","citation_count":19,"is_preprint":false},{"pmid":"36364454","id":"PMC_36364454","title":"Antibacterial Effect of Cell-Free Supernatant from Lactobacillus pentosus L-36 against Staphylococcus aureus from Bovine Mastitis.","date":"2022","source":"Molecules (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/36364454","citation_count":19,"is_preprint":false},{"pmid":"25119672","id":"PMC_25119672","title":"Roles of Ebp2 and ribosomal protein L36 in ribosome biogenesis in Saccharomyces cerevisiae.","date":"2014","source":"Current genetics","url":"https://pubmed.ncbi.nlm.nih.gov/25119672","citation_count":16,"is_preprint":false},{"pmid":"11168885","id":"PMC_11168885","title":"The metal binding properties of the CCCH motif of the 50S ribosomal protein L36 from Thermus thermophilus.","date":"2001","source":"The journal of peptide research : official journal of the American Peptide Society","url":"https://pubmed.ncbi.nlm.nih.gov/11168885","citation_count":15,"is_preprint":false},{"pmid":"15747135","id":"PMC_15747135","title":"Modulation of zinc- and cobalt-binding affinities through changes in the stability of the zinc ribbon protein L36.","date":"2005","source":"Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15747135","citation_count":9,"is_preprint":false},{"pmid":"33734578","id":"PMC_33734578","title":"Knockdown of RpL36 in testes impairs spermatogenesis in Drosophila melanogaster.","date":"2021","source":"Journal of experimental zoology. Part B, Molecular and developmental evolution","url":"https://pubmed.ncbi.nlm.nih.gov/33734578","citation_count":8,"is_preprint":false},{"pmid":"3095423","id":"PMC_3095423","title":"Monoclonal antibodies, L-35 and L-36, define novel T cell activation antigens.","date":"1986","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/3095423","citation_count":7,"is_preprint":false},{"pmid":"28090422","id":"PMC_28090422","title":"Elevated levels of ribosomal proteins eL36 and eL42 control expression of Hsp90 in rhabdomyosarcoma.","date":"2016","source":"Translation (Austin, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/28090422","citation_count":6,"is_preprint":false},{"pmid":"38367942","id":"PMC_38367942","title":"The m6A reader IGF2BP1 attenuates the stability of RPL36 and cell proliferation to mediate benzene hematotoxicity by recognizing m6A modification.","date":"2024","source":"Toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/38367942","citation_count":6,"is_preprint":false},{"pmid":"11409180","id":"PMC_11409180","title":"Primary structure and transcription patterns of RPL36, a ribosomal protein-encoding gene of the mycoparasitic fungus, Trichoderma hamatum.","date":"2001","source":"Current genetics","url":"https://pubmed.ncbi.nlm.nih.gov/11409180","citation_count":5,"is_preprint":false},{"pmid":"39700429","id":"PMC_39700429","title":"Ribosomal protein L36-mediated selective loading of microRNA-4432 into extracellular vesicles contributes to perivascular cell dysfunction in venous malformations.","date":"2025","source":"The British journal of dermatology","url":"https://pubmed.ncbi.nlm.nih.gov/39700429","citation_count":5,"is_preprint":false},{"pmid":"8484789","id":"PMC_8484789","title":"The primary structure of rat ribosomal protein L36.","date":"1993","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/8484789","citation_count":5,"is_preprint":false},{"pmid":"37865285","id":"PMC_37865285","title":"The Role of Ribosomal Proteins eL15 and eL36 in the Early Steps of Yeast 60S Ribosomal Subunit Assembly.","date":"2023","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/37865285","citation_count":3,"is_preprint":false},{"pmid":"15620217","id":"PMC_15620217","title":"Primary structure of dihydrofolate reductase and mitochondrial ribosomal protein L36 genes from the basidiomycete Coprinus cinereus.","date":"2004","source":"DNA sequence : the journal of DNA sequencing and mapping","url":"https://pubmed.ncbi.nlm.nih.gov/15620217","citation_count":0,"is_preprint":false},{"pmid":"42218987","id":"PMC_42218987","title":"A novel peptide mR63-77 from Rpl36 protein showing potent antibacterial activities.","date":"2026","source":"International journal of antimicrobial agents","url":"https://pubmed.ncbi.nlm.nih.gov/42218987","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13498,"output_tokens":4481,"usd":0.053854,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12602,"output_tokens":4201,"usd":0.084017,"stage2_stop_reason":"end_turn"},"total_usd":0.137871,"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\": 1977,\n      \"finding\": \"RPL36 (L36) protein was isolated and purified from the 60S ribosomal large subunit of rat liver ribosomes, establishing it as a bona fide component of the eukaryotic large ribosomal subunit. Molecular weight and amino acid composition were determined.\",\n      \"method\": \"Ion exchange chromatography, gel filtration, SDS-PAGE, amino acid composition analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct biochemical isolation and characterization, replicated across multiple labs over decades\",\n      \"pmids\": [\"863909\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"The primary amino acid sequence of rat RPL36 was determined: 104 amino acids (N-terminal Met cleaved post-translationally), MW ~12,128 Da, related to yeast ribosomal protein YL39. The mRNA is ~500 nt and there are 8–11 gene copies in the rat genome.\",\n      \"method\": \"cDNA sequencing, Southern blotting, Northern blotting\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct sequencing and structural determination with multiple orthogonal methods\",\n      \"pmids\": [\"8484789\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"The solution NMR structure of ribosomal protein L36 from Thermus thermophilus revealed a zinc-ribbon-like fold: a triple-stranded antiparallel beta-sheet with a zinc-binding site (C-X2-C-X12-C-X4-H motif) coordinating zinc via three cysteines and one histidine (N-delta1). EXAFS confirmed equimolar zinc content. The electrostatic surface and conserved basic residues suggest a large L36-rRNA interaction interface. The fold topology resembles zinc-ribbon domains of transcription factors TFIIB and hTFIIS.\",\n      \"method\": \"Solution NMR structure determination, EXAFS spectroscopy, simulated annealing with NOE/dihedral restraints\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution NMR structure with orthogonal EXAFS validation of metal coordination\",\n      \"pmids\": [\"10656825\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"The CCCH zinc-finger motif (C-X2-C-X12-C-X4-H) of Thermus thermophilus L36 binds metal ions with differential affinities in the order Co(II) > Hg(II) > Zn(II), as measured on a synthetic 26-mer peptide containing this motif.\",\n      \"method\": \"Solid-phase peptide synthesis, circular dichroism, capillary electrophoresis, electrospray ionization mass spectrometry, spectroscopic metal-binding assays\",\n      \"journal\": \"The journal of peptide research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro biochemical characterization on synthetic peptide, single lab, orthogonal spectroscopic methods but isolated peptide not full protein\",\n      \"pmids\": [\"11168885\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Metal-binding affinities of L36 zinc-ribbon protein are modulated by mutations in the beta-sheet hydrophobic cluster and beta-hairpin turn without changing the overall fold. Specifically: His32→Cys decreases affinity for both Zn(II) and Co(II); Tyr24→Trp increases both affinities; His20→Asn also increases both affinities. The protein normally binds Zn(II) ~2800-fold more tightly than Co(II).\",\n      \"method\": \"UV-vis spectroscopy metal-binding assays, circular dichroism, size-exclusion chromatography, 1D and 2D 1H NMR, site-directed mutagenesis\",\n      \"journal\": \"Journal of biological inorganic chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro mutagenesis with multiple orthogonal biophysical methods, single lab\",\n      \"pmids\": [\"15747135\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Functional cloning demonstrated that transfection of RPL36 cDNA conferred 2.5- to 3-fold cisplatin resistance in KB-3-1 cells, identifying RPL36 as a gene directly contributing to cisplatin resistance (confirmed in two independent transfection experiments).\",\n      \"method\": \"Retroviral cDNA library functional cloning, cisplatin selection, clonogenic assays, cDNA transfection\",\n      \"journal\": \"Molecular pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional gain-of-function cloning with defined phenotypic readout, replicated in two independent transfection experiments, single lab\",\n      \"pmids\": [\"16394183\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In Saccharomyces cerevisiae, RPL36A/B (encoding L36a/b) is required for processing of 27SA2, 27SA3, and 27SBL pre-rRNAs during 60S ribosomal subunit biogenesis. RPL36A/B overexpression suppresses ebp2 mutant growth defects. Two-hybrid analysis showed L36a/b physically interacts with the assembly factor Ebp2, as well as ribosomal proteins L34a/b and L8 (which are adjacent to the 3′ end of 5.8S rRNA in mature ribosomes).\",\n      \"method\": \"Genetic suppression analysis (multicopy suppressor screen), synthetic growth enhancement, primer-extension pre-rRNA processing analysis, yeast two-hybrid\",\n      \"journal\": \"Current genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple genetic and molecular methods (suppressor screen, pre-rRNA processing, two-hybrid) in single lab, yeast ortholog\",\n      \"pmids\": [\"25119672\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In a zebrafish pancreatic cancer model, rpl36 heterozygous loss (haploinsufficiency) accelerated KRAS(G12V)-driven tumor progression and decreased survival in pancreatic acinar cells, establishing rpl36 as a haploinsufficient tumor suppressor in this context. rpl23a did not show this effect, indicating specificity.\",\n      \"method\": \"Zebrafish genetic model (rpl36 hi1807/+ heterozygous mutants crossed with ptf1a:gal4VP16;UAS:GFP-KRAS(G12V) transgenic fish), survival analysis, genetic epistasis\",\n      \"journal\": \"Zebrafish\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo genetic loss-of-function with defined oncogenic context and survival endpoint, zebrafish ortholog, single lab\",\n      \"pmids\": [\"25380065\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Ribosomal protein eL36 (RPL36) modulates translation of Hsp90α mRNA. Elevated eL36 (and eL42) levels in rhabdomyosarcoma drive high Hsp90 expression and modulate sensitivity to the Hsp90 inhibitor 17-AAG. Polysome profiling showed Hsp90α mRNA is selectively translated under heat stress conditions where global translation is inhibited.\",\n      \"method\": \"Polysome profiling, RNA interference/knockdown, Hsp90 inhibitor sensitivity assay (17-AAG), rhabdomyosarcoma cell lines\",\n      \"journal\": \"Translation (Austin, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — polysome profiling with functional inhibitor sensitivity readout, single lab, two orthogonal methods\",\n      \"pmids\": [\"28090422\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In glioma cells, RPL36 promotes cell proliferation and G1/S cell cycle progression. STAT1 was identified by mass spectrometry as a protein that interacts with both lncRNA PLAC2 and the RPL36 promoter, binding at the RPL36 promoter to regulate its expression. Nuclear PLAC2 binds STAT1 and interacts with the RPL36 promoter, while cytoplasmic PLAC2 inhibits STAT1 nuclear translocation, thereby decreasing RPL36 expression and inducing cell cycle arrest.\",\n      \"method\": \"Mass spectrometry (co-immunoprecipitation-MS), cell proliferation assays, cell cycle analysis (flow cytometry), nuclear/cytoplasmic fractionation, ChIP/promoter binding assays, siRNA knockdown\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mass spectrometry identification of STAT1 interaction, cell cycle functional readout, multiple methods, single lab\",\n      \"pmids\": [\"28922548\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In zinc-deficient E. coli, the zinc-binding ribosomal protein L36 (encoded by rpmJ) is replaced at its ribosomal binding site by the paralog YkgO (expressed from the ykgM operon under Zur repressor control). Copy numbers of L36 and YkgO sum to 1, indicating they share a single binding site. Loss of rpmJ impairs late assembly of the 50S particle, reduces in vitro translation, and causes growth defects; YkgO rescues these functions in zur mutant cells.\",\n      \"method\": \"Genetic deletion (rpmJ null mutants), suppressor mutant isolation (zur mutations), ribosome fractionation, in vitro translation assays, copy number quantitation\",\n      \"journal\": \"Genes to cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and biochemical analysis with defined functional readouts in E. coli, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"32559334\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Alt-RPL36, a protein co-encoded with human RPL36 from an alternative ORF in the same transcript, partially localizes to the endoplasmic reticulum and interacts with TMEM24 (a PI transfer protein). Knockout of alt-RPL36 increases plasma membrane PI(4,5)P2 levels, upregulates PI3K-AKT-mTOR signaling, and increases cell size. Alt-RPL36 contains four phosphoserine residues; point mutations abolishing these phosphorylations eliminate TMEM24 interaction and consequently ablate alt-RPL36 effects on PI3K signaling and cell size.\",\n      \"method\": \"Alternative ORF detection, co-immunoprecipitation, knockout (CRISPR), PI(4,5)P2 biosensor imaging, PI3K-AKT-mTOR signaling assays (phospho-Western), cell size measurement, phosphosite mutagenesis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (Co-IP, KO, PI biosensor, mutagenesis, signaling assays) in a single rigorous study\",\n      \"pmids\": [\"33479206\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Knockdown of RpL36 in Drosophila melanogaster testes impairs spermatogenesis: causes smaller testes, reduced germ cells (including germ stem cells), enlarged hub cell clusters, fewer mature sperm, increased apoptosis (TUNEL signal in non-germ cells), and reduced pH3-positive (mitotic) germ cells. Transcriptome analysis of knockdown testes showed altered expression of genes in cell death, cell cycle progression, and JAK/STAT signaling pathway.\",\n      \"method\": \"RNAi knockdown (testis-specific), immunofluorescence (Vasa, pH3), TUNEL assay, fertility assay (egg hatch rate), gene expression analysis\",\n      \"journal\": \"Journal of experimental zoology. Part B, Molecular and developmental evolution\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo loss-of-function with multiple cellular phenotype readouts, Drosophila ortholog, single lab\",\n      \"pmids\": [\"33734578\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In Saccharomyces cerevisiae, depletion of eL36 not only blocks its own assembly into pre-60S particles but also impairs assembly of neighboring ribosomal proteins eL15 and eL8 into early pre-60S particles, and causes loss of most A3- and B-factors (assembly factors for 27SA3 and 27SB pre-rRNA processing). These results indicate that eL36, together with eL8 and eL15, is prerequisite for shaping domain I of 5.8S/25S rRNA within early pre-60S particles.\",\n      \"method\": \"Conditional depletion (in vivo), pre-rRNA processing analysis, mass spectrometry analysis of pre-60S particle composition, genetic/biochemical epistasis\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo depletion with MS-based particle composition analysis and pre-rRNA processing, yeast ortholog, single lab\",\n      \"pmids\": [\"37865285\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"m6A modification of RPL36 mRNA reduces its stability and thereby decreases RPL36 expression. The m6A reader IGF2BP1 directly binds RPL36 mRNA to attenuate this destabilization, maintaining RPL36 expression and cell proliferation. In benzene-exposed cells/animals, reduced IGF2BP1 leads to hypomethylation and reduced RPL36 expression, impairing cell proliferation; IGF2BP1 overexpression rescues RPL36 mRNA levels and proliferation.\",\n      \"method\": \"m6A transcriptome-wide sequencing (MeRIP-seq), RNA stability assays, IGF2BP1 overexpression (in vitro and in vivo mouse model), mRNA expression analysis, cell proliferation assays\",\n      \"journal\": \"Toxicology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — transcriptome-wide m6A mapping combined with in vitro and in vivo functional rescue, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"38367942\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RPL36 functions as an RNA-binding protein and sorting regulator of microRNA-4432 into extracellular vesicles in TIE2(L914F)-mutant endothelial cells (venous malformation model). RPL36-mediated selective loading of miR-4432 into EVs contributes to inhibition of perivascular cell differentiation, adhesion, and proliferation, identified by miRNA pulldown and RNA interference.\",\n      \"method\": \"RNA sequencing (miRNA profiling of cells and EVs), miRNA pulldown, RNA interference, functional assays (differentiation, adhesion, proliferation of umbilical cord stem cells)\",\n      \"journal\": \"The British journal of dermatology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — miRNA pulldown plus RNAi with defined functional readouts, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"39700429\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RPL36 is a zinc-ribbon domain-containing component of the 60S ribosomal large subunit that binds rRNA via conserved basic residues, is required for pre-rRNA processing (27SA2/27SA3/27SB) and late 50S/60S assembly cooperatively with neighboring ribosomal proteins eL8 and eL15, promotes G1/S cell cycle progression and cell proliferation, confers cisplatin resistance, and acts as a haploinsufficient tumor suppressor in the context of oncogenic KRAS; additionally, RPL36 selectively modulates translation of Hsp90α mRNA, functions as an RNA-binding protein that sorts miR-4432 into extracellular vesicles, and its mRNA stability is regulated by m6A modification read by IGF2BP1, while a co-encoded alternative ORF (alt-RPL36) independently regulates PI3K-AKT-mTOR signaling through phosphoserine-dependent interaction with the PI transfer protein TMEM24 at the endoplasmic reticulum.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPL36 (eL36) is a zinc-ribbon-domain protein component of the eukaryotic 60S large ribosomal subunit, originally isolated as a ~12 kDa basic protein from rat liver ribosomes [#0, #1]. Structural work on the bacterial counterpart established its defining fold: a triple-stranded antiparallel beta-sheet stabilized by a CCCH zinc-binding motif (C-X2-C-X12-C-X4-H) whose conserved basic surface forms an extensive rRNA-interaction interface [#2]. During subunit biogenesis, eL36 is required for processing of 27SA2, 27SA3, and 27SB pre-rRNAs and acts cooperatively with the neighboring ribosomal proteins eL8 and eL15 to shape domain I of 5.8S/25S rRNA in early pre-60S particles, with its depletion also blocking recruitment of A3- and B-class assembly factors [#6, #13]. Beyond its core ribosomal role, RPL36 promotes cell proliferation and G1/S cell cycle progression, a function controlled at the promoter by STAT1 [#9], and its mRNA stability is set by m6A modification read by IGF2BP1 [#14]. RPL36 contributes to cisplatin resistance [#5] and behaves as a haploinsufficient tumor suppressor that accelerates KRAS-driven pancreatic tumorigenesis when lost [#7]. It also exhibits extra-ribosomal activities, selectively modulating Hsp90\\u03b1 mRNA translation [#8] and acting as an RNA-binding protein that sorts miR-4432 into extracellular vesicles [#15]. Notably, an alternative ORF in the same transcript encodes alt-RPL36, a distinct ER-associated protein that, through phosphoserine-dependent binding to the PI transfer protein TMEM24, restrains plasma-membrane PI(4,5)P2 levels and PI3K-AKT-mTOR signaling [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 1977,\n      \"claim\": \"Established RPL36 as a genuine constituent of the eukaryotic large ribosomal subunit rather than a contaminant, defining the physical object all later work concerns.\",\n      \"evidence\": \"Biochemical purification from rat liver 60S subunits with SDS-PAGE and amino acid composition analysis\",\n      \"pmids\": [\"863909\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No sequence or structural information at this stage\", \"Functional role within the ribosome undefined\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Provided the primary sequence and gene-copy context, anchoring RPL36 to the conserved YL39 ribosomal protein family and enabling molecular study.\",\n      \"evidence\": \"cDNA sequencing with Southern and Northern blotting in rat\",\n      \"pmids\": [\"8484789\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No three-dimensional structure\", \"rRNA contacts not mapped\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Resolved the fold as a zinc-ribbon with a CCCH zinc-coordination site and a basic rRNA-binding surface, explaining how the protein engages rRNA.\",\n      \"evidence\": \"Solution NMR structure and EXAFS metal validation of Thermus thermophilus L36\",\n      \"pmids\": [\"10656825\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure from bacterial ortholog, not human protein\", \"rRNA interface inferred from electrostatics, not co-structure\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Defined the determinants of metal selectivity in the zinc-ribbon, showing the fold strongly favors Zn(II) and that specific residues tune affinity without disrupting topology.\",\n      \"evidence\": \"Site-directed mutagenesis with UV-vis, CD, and NMR metal-binding assays on the bacterial protein (extends 2001 peptide work)\",\n      \"pmids\": [\"15747135\", \"11168885\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vitro biophysics on bacterial protein/peptide\", \"Physiological relevance of metal selectivity in the assembled ribosome untested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Placed RPL36 in the 60S biogenesis pathway by showing it is needed for specific pre-rRNA processing steps and physically links to assembly factor Ebp2 and neighboring r-proteins.\",\n      \"evidence\": \"Multicopy suppressor screen, primer-extension pre-rRNA analysis, and yeast two-hybrid in S. cerevisiae\",\n      \"pmids\": [\"25119672\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interaction order and direct vs. indirect contacts not resolved\", \"Yeast ortholog; human pathway not directly tested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstrated a context-specific tumor-suppressor role, with haploinsufficient rpl36 loss accelerating oncogenic KRAS-driven cancer, distinguishing it from a generic ribosomal protein.\",\n      \"evidence\": \"Zebrafish heterozygous mutant crossed to KRAS(G12V) pancreatic model with survival analysis\",\n      \"pmids\": [\"25380065\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking reduced RPL36 to tumor acceleration unknown\", \"Specificity to KRAS context not generalized\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identified an extra-ribosomal translational specialization, with RPL36 levels selectively modulating Hsp90\\u03b1 mRNA translation and chaperone-inhibitor sensitivity.\",\n      \"evidence\": \"Polysome profiling and Hsp90 inhibitor sensitivity assays after knockdown in rhabdomyosarcoma cells\",\n      \"pmids\": [\"28090422\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of mRNA selectivity not defined\", \"Whether effect requires intact ribosome vs. free RPL36 unclear\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Connected RPL36 expression to proliferation control via an upstream STAT1/lncRNA regulatory axis acting at the RPL36 promoter.\",\n      \"evidence\": \"Co-IP-MS, ChIP/promoter binding, fractionation, and cell-cycle assays in glioma cells\",\n      \"pmids\": [\"28922548\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs. indirect STAT1 promoter occupancy not fully separated\", \"Downstream proliferation effectors of RPL36 not identified\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Confirmed the conserved structural-zinc and late-assembly role through bacterial paralog substitution, showing L36 occupies a single binding site essential for 50S maturation.\",\n      \"evidence\": \"rpmJ deletion, ykgM/YkgO paralog rescue, ribosome fractionation, and in vitro translation in E. coli\",\n      \"pmids\": [\"32559334\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Bacterial system; eukaryotic zinc-homeostasis link untested\", \"Whether human RPL36 has an analogous paralog switch unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Revealed a dual-coding transcript in which an alternative ORF (alt-RPL36) acts independently of ribosome biogenesis to restrain PI3K-AKT-mTOR signaling via phosphoserine-dependent TMEM24 binding at the ER.\",\n      \"evidence\": \"Alt-ORF detection, Co-IP, CRISPR knockout, PI(4,5)P2 biosensor imaging, phosphosite mutagenesis, and signaling assays\",\n      \"pmids\": [\"33479206\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kinase phosphorylating alt-RPL36 not identified\", \"Relationship between canonical RPL36 and alt-RPL36 functions not integrated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed RPL36 is required in vivo for tissue homeostasis, with knockdown disrupting spermatogenesis through altered cell death, cell cycle, and JAK/STAT gene expression.\",\n      \"evidence\": \"Testis-specific RNAi, immunofluorescence, TUNEL, and transcriptome analysis in Drosophila\",\n      \"pmids\": [\"33734578\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phenotype may reflect general ribosome insufficiency\", \"Direct targets of RPL36 in germline not defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined post-transcriptional control of RPL36 abundance, showing m6A destabilizes its mRNA while the reader IGF2BP1 protects the transcript to sustain proliferation.\",\n      \"evidence\": \"MeRIP-seq, RNA stability assays, and IGF2BP1 gain-of-function rescue in vitro and in benzene-exposed mice\",\n      \"pmids\": [\"38367942\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Writer/eraser enzymes setting the m6A mark not identified\", \"Whether proliferation effect is ribosomal or extra-ribosomal unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended RPL36's RNA-binding repertoire to selective miRNA cargo sorting, loading miR-4432 into extracellular vesicles to influence perivascular cell behavior.\",\n      \"evidence\": \"miRNA pulldown, RNAi, and functional differentiation/adhesion/proliferation assays in TIE2-mutant endothelial cells\",\n      \"pmids\": [\"39700429\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"RNA-binding determinants of RPL36 for miR-4432 not mapped\", \"Generality of EV-sorting function beyond venous malformation context unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RPL36's canonical ribosomal role mechanistically connects to its extra-ribosomal activities (selective translation, EV miRNA sorting, tumor suppression) and to the independently acting alt-RPL36 remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of human RPL36 within the 60S subunit in the corpus\", \"Mechanism partitioning free vs. ribosome-bound RPL36 functions undefined\", \"Causal link between RPL36 dosage and KRAS-context tumor suppression unexplained\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [8, 15]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 2, 13]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [6, 13]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"complexes\": [\n      \"60S large ribosomal subunit\"\n    ],\n    \"partners\": [\n      \"eL8\",\n      \"eL15\",\n      \"Ebp2\",\n      \"TMEM24\",\n      \"STAT1\",\n      \"IGF2BP1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":7,"faith_total":7,"faith_pct":100.0}}