{"gene":"RPL35","run_date":"2026-06-10T07:46:26","timeline":{"discoveries":[{"year":1977,"finding":"RPL35 (L35) was isolated and purified as a component of the 60S large ribosomal subunit from rat liver ribosomes, with molecular weight estimated by SDS-PAGE and amino acid composition 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 purification and characterization, replicated across multiple papers from the same era","pmids":["863909"],"is_preprint":false},{"year":1990,"finding":"The primary structure of rat ribosomal protein L35 was determined: 122 amino acids (N-terminal methionine removed post-translationally), molecular weight 14,412 Da; the protein is related to archaebacterial L33/L29E and E. coli L29, and contains a possible internal duplication of 11 residues.","method":"cDNA sequencing, N-terminal amino acid sequencing, Southern blotting","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct protein sequencing confirmed by cDNA sequence, multiple orthogonal methods","pmids":["2322279"],"is_preprint":false},{"year":2008,"finding":"Human RPL35 carries a 54 aa eukaryotic expansion segment (ES) at the C-terminal end. The first 25 aa of the ES are essential for nuclear import of the protein. The last 29 residues of the ES are not required for ribosome structural or translational functions but serve as a contact site for ribosomal docking to the endoplasmic reticulum.","method":"In vivo recombinant ribosome analysis, deletion mutagenesis, subcellular localization assays","journal":"Biochemistry and cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional mutagenesis with defined phenotypic readouts (nuclear import, ER docking, translation), single lab","pmids":["18523488"],"is_preprint":false},{"year":2010,"finding":"In yeast (Saccharomyces cerevisiae), depletion of ribosomal protein L35 results in a deficit in 60S ribosomal subunits, half-mer polysomes, and a strong delay in processing of 27SB to 7S pre-rRNAs (cleavage at ITS2 site C2). L35 assembles in the nucleolus and associates with early pre-60S ribosomal particles. Loss of L35 also blocks release of pre-60S particles from nucleolus to nucleoplasm and mildly delays G1 phase of the cell cycle.","method":"In vivo depletion, pulse-chase labeling, northern hybridization, primer extension, flow cytometry, deletion mutant analysis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (pulse-chase, northern, primer extension, flow cytometry) in a single rigorous yeast study establishing specific pre-rRNA processing role","pmids":["20392820"],"is_preprint":false},{"year":2015,"finding":"RPL35 controls ribosomal translational elongation of β-casein (CSN2) by directly interacting with eukaryotic translational elongation factor 2 (eEF2), with eEF2 acting downstream of RPL35. RPL35 also controls secretion of CSN2 by localizing it to the ER. Methionine promotes RPL35 expression, and RPL35 mediates the methionine signal to regulate CSN2 expression in bovine mammary epithelial cells.","method":"Co-immunoprecipitation, colocalization, FRET, gene mutation/overexpression/knockdown","journal":"Archives of biochemistry and biophysics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, FRET, and mutagenesis in a single lab, multiple orthogonal methods","pmids":["26297660"],"is_preprint":false},{"year":2019,"finding":"RPL35 binds the long noncoding RNA lncNB1, and this interaction enhances E2F1 protein synthesis (translational), leading to DEPDC1B gene transcription. DEPDC1B (GTPase-activating protein) then induces ERK phosphorylation and N-Myc protein stabilization. RPL35 knockdown reduces neuroblastoma cell clonogenic capacity.","method":"RNA pulldown, Co-IP, loss-of-function (knockdown), reporter assays, in vivo tumor regression","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNA-protein interaction established by pulldown, functional epistasis by knockdown, multiple orthogonal methods in a single lab","pmids":["31690716"],"is_preprint":false},{"year":2021,"finding":"RPL35 knockdown in neuroblastoma cells decreases aerobic glycolysis and increases mitochondrial respiration, decreases HIF1α expression (mRNA and protein), and negatively regulates ERK pathway activity. RPL35 modulates aerobic glycolysis in part through the RPL35/ERK/HIF1α axis.","method":"siRNA knockdown, Western blot, metabolic assays (glycolysis/respiration), qPCR","journal":"American journal of cancer research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, knockdown with phenotypic readout but pathway placement inferred without epistasis rescue experiments","pmids":["34873488"],"is_preprint":false},{"year":2021,"finding":"RPL35 interacts directly with the Mycoplasma genitalium adhesin protein MgPa (verified by far-Western blot and co-localization), and this interaction promotes expression of EIF2, SRP68, SERBP1, RPL35A, EGF, and TGF-β, and enhances urothelial cell proliferation.","method":"T7 phage-display library screening, far-Western blot, co-localization, TMT proteomics, qRT-PCR, MTT assay","journal":"Pathogens","confidence":"Low","confidence_rationale":"Tier 3 / Weak — interaction confirmed by far-Western and co-localization, but downstream mechanism is correlative; single lab","pmids":["34832605"],"is_preprint":false},{"year":2021,"finding":"Drug development study using NMR titration identified that atazanavir and artesunate bind to human RPL35 near the N-terminus; NMR chemical shift mapping revealed the amino acids at the ligand-binding sites, including a binding cluster accessible when RPL35 is integrated into the ribosome.","method":"Molecular docking, NMR spectroscopy (chemical shift titration)","journal":"Skin pharmacology and physiology","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — NMR with site mapping is a structural method with chemical validation, but functional consequence of binding not confirmed in vivo; single study","pmids":["33823521"],"is_preprint":false},{"year":2022,"finding":"DDX10 interacts with RPL35 (identified by LC-MS/MS and confirmed by Co-IP), and DDX10 is proposed to regulate CRC cell proliferation and metastasis via splicing-related mechanisms involving RPL35.","method":"LC-MS/MS, Co-IP","journal":"Cancer cell international","confidence":"Low","confidence_rationale":"Tier 3 / Weak — interaction identified by mass spectrometry and confirmed by single Co-IP, no detailed mechanistic follow-up for RPL35 specifically","pmids":["35109823"],"is_preprint":false},{"year":2024,"finding":"RPL35 protein expression is reduced in chondrocytes under excessive mechanical loading. RPL35 knockdown alone induces chondrocyte senescence, decreases anabolic markers, and increases catabolic markers in part through activation of the Hedgehog (Hh)/Gli1 pathway. Intra-articular overexpression of RPL35 protects against cartilage degeneration in a mouse OA model.","method":"RNA sequencing, siRNA knockdown, adenovirus-mediated overexpression, Western blot, immunostaining, in vivo mouse OA model","journal":"Journal of orthopaedic translation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined pathway (Hh/Gli1) placement validated in vitro and in vivo, single lab","pmids":["38596341"],"is_preprint":false},{"year":2024,"finding":"TENT5A interacts with RPL35 (Co-IP + GST pull-down confirmed by mass spectrometry) and negatively regulates RPL35 protein stability. The EGR1/TENT5A/RPL35 axis is involved in ribosome biogenesis and negatively regulates the mTOR pathway in hepatocellular carcinoma cells.","method":"Co-immunoprecipitation, GST pull-down, mass spectrometry, chromatin immunoprecipitation, dual-luciferase reporter assay, gain/loss-of-function experiments","journal":"Cellular oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and GST pulldown confirming interaction, plus functional pathway placement, single lab","pmids":["39570560"],"is_preprint":false},{"year":2025,"finding":"GADD45GIP1 interacts with RPL35 (identified by IP/LC-MS/MS, ranked second among 263 interacting proteins) and inhibits ubiquitin-mediated proteasomal degradation of RPL35. RPL35 knockdown activates the PERK-eIF2α ER stress pathway, increases ER stress, and reduces osteosarcoma cell viability. Overexpression of RPL35 counteracts the decrease in cell viability caused by GADD45GIP1 knockdown.","method":"Immunoprecipitation, LC-MS/MS, siRNA knockdown, overexpression rescue, Western blot for ubiquitination/PERK/eIF2α","journal":"Cancer cell international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — IP/MS-confirmed interaction, epistasis rescue experiment, ubiquitination measurement, single lab","pmids":["40604925"],"is_preprint":false},{"year":2025,"finding":"RPL35 functions as an antiviral host protein against FMDV by directly interacting with the FMDV structural protein VP2 and recruiting the E3 ubiquitin ligase AMFR to mediate K48-linked polyubiquitination and proteasomal degradation of VP2. The Lys217 residue of VP2 is critical for this RPL35-mediated antiviral activity. FMDV counteracts this by inducing degradation of KPNA3, thereby blocking RPL35 nuclear translocation.","method":"Co-IP, proteomic screen, ubiquitination assay, site-directed mutagenesis (VP2-K217R recombinant virus), KPNA3 knockdown/degradation assay","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — interaction and ubiquitination confirmed by Co-IP and mutant virus, multiple orthogonal methods in single study; not yet independently replicated","pmids":["41065387"],"is_preprint":false}],"current_model":"RPL35 (uL29/L35) is a structural component of the 60S ribosomal large subunit required for 27SB pre-rRNA processing and early pre-60S particle biogenesis; its eukaryotic C-terminal expansion segment mediates nuclear import (first 25 aa) and ER docking (last 29 aa), while its interaction with eEF2 controls translational elongation. Beyond its ribosomal role, RPL35 participates in extra-ribosomal functions: it binds lncNB1 to enhance E2F1 translation and N-Myc stabilization via ERK, recruits AMFR E3 ligase to ubiquitinate and degrade the FMDV capsid protein VP2 (antiviral), is stabilized by GADD45GIP1 to modulate ER stress via PERK/eIF2α, and is regulated in chondrocytes through the Hedgehog/Gli1 pathway; its protein stability is also regulated by TENT5A-dependent mechanisms in the EGR1/TENT5A/RPL35/mTOR axis."},"narrative":{"mechanistic_narrative":"RPL35 (uL29/L35) is a structural protein of the 60S large ribosomal subunit that is also required for early large-subunit biogenesis [PMID:863909, PMID:20392820]. First purified from rat liver ribosomes and sequenced as a 122-residue protein related to archaebacterial L33/L29E and E. coli L29 [PMID:863909, PMID:2322279], it assembles in the nucleolus on early pre-60S particles, and its depletion in yeast causes a deficit of 60S subunits, a strong delay in 27SB-to-7S pre-rRNA processing at ITS2 site C2, and a block in pre-60S nucleolus-to-nucleoplasm release [PMID:20392820]. In eukaryotes the protein carries a 54-aa C-terminal expansion segment whose first 25 residues are essential for nuclear import while its last 29 residues mediate ribosome docking to the endoplasmic reticulum [PMID:18523488]. RPL35 directly binds elongation factor eEF2 to control translational elongation and ER-localized secretion of nascent protein [PMID:26297660]. Beyond the ribosome, RPL35 has acquired extra-ribosomal regulatory roles: it binds the lncRNA lncNB1 to enhance E2F1 translation and drive a DEPDC1B–ERK–N-Myc axis supporting neuroblastoma proliferation [PMID:31690716], it acts as an antiviral host factor that recruits the E3 ligase AMFR to mediate K48-linked polyubiquitination and proteasomal degradation of the FMDV capsid protein VP2 [PMID:41065387], and its own stability is set by competing factors—negatively by TENT5A within an EGR1/TENT5A/RPL35/mTOR axis [PMID:39570560] and positively by GADD45GIP1, which blocks ubiquitin-mediated degradation of RPL35 and thereby restrains the PERK–eIF2α ER stress pathway [PMID:40604925]. RPL35 also protects chondrocytes against senescence and cartilage degeneration via suppression of the Hedgehog/Gli1 pathway [PMID:38596341].","teleology":[{"year":1977,"claim":"Established that L35 is a discrete, purifiable protein component of the eukaryotic 60S large ribosomal subunit, defining the molecule biochemically.","evidence":"Ion-exchange/gel-filtration purification, SDS-PAGE and amino acid composition from rat liver ribosomes","pmids":["863909"],"confidence":"High","gaps":["No sequence or structural position within the subunit","No functional role assigned"]},{"year":1990,"claim":"Resolved the primary structure and evolutionary relationships of the protein, placing it in the L29/L33E family and revealing an internal sequence duplication.","evidence":"cDNA and N-terminal protein sequencing with Southern blotting","pmids":["2322279"],"confidence":"High","gaps":["Functional significance of the internal duplication unknown","No mechanistic role established"]},{"year":2008,"claim":"Showed that the eukaryote-specific C-terminal expansion segment partitions distinct trafficking functions—nuclear import versus ER docking—separable from core ribosomal/translational function.","evidence":"Recombinant ribosome analysis with deletion mutagenesis and subcellular localization assays","pmids":["18523488"],"confidence":"Medium","gaps":["Import receptor not identified here","Single lab; structural basis of ER docking not resolved"]},{"year":2010,"claim":"Defined the precise biogenesis role: L35 assembles in the nucleolus on early pre-60S particles and is required for 27SB pre-rRNA processing and pre-60S nuclear export.","evidence":"Yeast depletion with pulse-chase, northern, primer extension and flow cytometry","pmids":["20392820"],"confidence":"High","gaps":["Direct interaction partners on pre-60S not mapped","Human ortholog biogenesis role inferred from yeast"]},{"year":2015,"claim":"Connected RPL35 to the elongation machinery and secretory output by demonstrating a direct eEF2 interaction controlling elongation and ER targeting of a secreted protein.","evidence":"Reciprocal Co-IP, FRET, colocalization and mutagenesis/knockdown in bovine mammary epithelial cells","pmids":["26297660"],"confidence":"Medium","gaps":["Generality beyond CSN2 substrate not tested","Mechanism of methionine-dependent regulation unclear"]},{"year":2019,"claim":"Revealed an extra-ribosomal, RNA-binding function in which RPL35 partners with lncNB1 to selectively enhance E2F1 translation and drive an oncogenic ERK/N-Myc cascade.","evidence":"RNA pulldown, Co-IP, knockdown, reporter assays and in vivo tumor regression in neuroblastoma","pmids":["31690716"],"confidence":"Medium","gaps":["Whether translational selectivity is ribosome-dependent unclear","Direct lncNB1-binding region of RPL35 not mapped"]},{"year":2021,"claim":"Extended the neuroblastoma role to metabolic control, placing RPL35 upstream of an ERK/HIF1α axis governing aerobic glycolysis.","evidence":"siRNA knockdown with metabolic assays, Western blot and qPCR","pmids":["34873488"],"confidence":"Low","gaps":["Pathway placement inferred without epistasis rescue","Single lab, correlative"]},{"year":2021,"claim":"Implicated RPL35 as a host target of a bacterial adhesin, linking the protein to proliferative signaling during Mycoplasma infection.","evidence":"Phage display, far-Western, colocalization, TMT proteomics and MTT in urothelial cells","pmids":["34832605"],"confidence":"Low","gaps":["Downstream effects correlative","No reciprocal validation of functional consequence"]},{"year":2021,"claim":"Provided structural ligand-binding information by mapping small-molecule (atazanavir, artesunate) contact sites on human RPL35.","evidence":"Molecular docking and NMR chemical-shift titration","pmids":["33823521"],"confidence":"Medium","gaps":["Functional consequence of binding not tested in vivo","Single study"]},{"year":2022,"claim":"Identified DDX10 as a physical interactor of RPL35 in colorectal cancer, hinting at a link between RPL35 and splicing-associated processes.","evidence":"LC-MS/MS and Co-IP","pmids":["35109823"],"confidence":"Low","gaps":["No mechanistic follow-up for RPL35 specifically","Single Co-IP without reciprocal validation"]},{"year":2024,"claim":"Established a protective role for RPL35 in chondrocyte homeostasis, where its loss promotes senescence via Hedgehog/Gli1 activation and its restoration limits OA cartilage degeneration.","evidence":"RNA-seq, siRNA knockdown, adenoviral overexpression and an in vivo mouse OA model","pmids":["38596341"],"confidence":"Medium","gaps":["Mechanism linking RPL35 to Hh/Gli1 not defined","Single lab"]},{"year":2024,"claim":"Defined RPL35 as a regulated node whose stability is negatively controlled by TENT5A within an EGR1/TENT5A/RPL35 axis that restrains mTOR signaling in hepatocellular carcinoma.","evidence":"Co-IP, GST pull-down, mass spectrometry, ChIP and luciferase reporter with gain/loss-of-function","pmids":["39570560"],"confidence":"Medium","gaps":["Mechanism of TENT5A-mediated destabilization unclear","Direct link of RPL35 to mTOR not resolved"]},{"year":2025,"claim":"Showed RPL35 protein abundance is set by ubiquitin-mediated turnover that GADD45GIP1 antagonizes, coupling RPL35 stability to control of the PERK-eIF2α ER stress response.","evidence":"IP/LC-MS/MS, siRNA knockdown, overexpression rescue and ubiquitination/PERK/eIF2α Western blots in osteosarcoma","pmids":["40604925"],"confidence":"Medium","gaps":["E3 ligase for RPL35 in this context not identified","Single lab"]},{"year":2025,"claim":"Demonstrated an antiviral effector function: RPL35 recruits AMFR to ubiquitinate and degrade the FMDV capsid protein VP2, a defense the virus evades by blocking RPL35 nuclear translocation.","evidence":"Co-IP, proteomic screen, ubiquitination assay, VP2-K217R recombinant virus and KPNA3 degradation assay","pmids":["41065387"],"confidence":"Medium","gaps":["Whether antiviral activity is ribosome-independent unclear","Not independently replicated"]},{"year":null,"claim":"How RPL35's core ribosomal function is mechanistically partitioned from its diverse extra-ribosomal roles—and what governs its differential engagement across these contexts—remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model integrating ribosomal and extra-ribosomal interfaces","Direct RNA- and protein-binding surfaces for extra-ribosomal partners unmapped","No human Mendelian disease link established in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[5]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[4]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[3]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2,13]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[2,4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[3]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[4]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[3]}],"complexes":["60S large ribosomal subunit","pre-60S ribosomal particle"],"partners":["EEF2","LNCNB1","AMFR","TENT5A","GADD45GIP1","DDX10","KPNA3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P42766","full_name":"Large ribosomal subunit protein uL29","aliases":["60S ribosomal protein L35"],"length_aa":123,"mass_kda":14.6,"function":"Component of the large ribosomal subunit (PubMed:12962325, PubMed:23636399, PubMed:32669547). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:12962325, PubMed:23636399, PubMed:32669547)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P42766/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPL35","classification":"Common Essential","n_dependent_lines":1207,"n_total_lines":1208,"dependency_fraction":0.9991721854304636},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000136942","cell_line_id":"CID000862","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleolus_gc","grade":2}],"interactors":[{"gene":"EIF2S3","stoichiometry":10.0},{"gene":"METAP2","stoichiometry":10.0},{"gene":"RACK1","stoichiometry":10.0},{"gene":"RBM8A","stoichiometry":10.0},{"gene":"RPL11","stoichiometry":10.0},{"gene":"RPL19","stoichiometry":10.0},{"gene":"RPL15","stoichiometry":10.0},{"gene":"RPS10;RPS10-NUDT3","stoichiometry":10.0},{"gene":"SRP72","stoichiometry":10.0},{"gene":"RPL4","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID000862","total_profiled":1310},"omim":[{"mim_id":"621189","title":"LONG INTERGENIC NONCODING RNA 2525; LINC02525","url":"https://www.omim.org/entry/621189"},{"mim_id":"618315","title":"RIBOSOMAL PROTEIN L35; RPL35","url":"https://www.omim.org/entry/618315"},{"mim_id":"618312","title":"DIAMOND-BLACKFAN ANEMIA 19; DBA19","url":"https://www.omim.org/entry/618312"},{"mim_id":"617649","title":"UBIQUITIN-CONJUGATING ENZYME E2 O; UBE2O","url":"https://www.omim.org/entry/617649"},{"mim_id":"105650","title":"DIAMOND-BLACKFAN ANEMIA 1; DBA1","url":"https://www.omim.org/entry/105650"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Endoplasmic reticulum","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPL35"},"hgnc":{"alias_symbol":["L35","uL29"],"prev_symbol":[]},"alphafold":{"accession":"P42766","domains":[{"cath_id":"1.10.287.310","chopping":"5-111","consensus_level":"high","plddt":94.9971,"start":5,"end":111}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P42766","model_url":"https://alphafold.ebi.ac.uk/files/AF-P42766-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P42766-F1-predicted_aligned_error_v6.png","plddt_mean":94.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPL35","jax_strain_url":"https://www.jax.org/strain/search?query=RPL35"},"sequence":{"accession":"P42766","fasta_url":"https://rest.uniprot.org/uniprotkb/P42766.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P42766/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P42766"}},"corpus_meta":[{"pmid":"10933704","id":"PMC_10933704","title":"Construction, phenotypic analysis, and immunogenicity of a UL5/UL29 double deletion mutant of herpes simplex virus 2.","date":"2000","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/10933704","citation_count":96,"is_preprint":false},{"pmid":"31690716","id":"PMC_31690716","title":"The long noncoding RNA lncNB1 promotes tumorigenesis by interacting with ribosomal protein RPL35.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/31690716","citation_count":84,"is_preprint":false},{"pmid":"1002715","id":"PMC_1002715","title":"Isolation of eukaryotic ribosomal proteins. 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1.","date":"1999","source":"The Journal of veterinary medical science","url":"https://pubmed.ncbi.nlm.nih.gov/10563297","citation_count":8,"is_preprint":false},{"pmid":"23237085","id":"PMC_23237085","title":"Prokaryotic expression and characteristics of duck enteritis virus UL29 gene.","date":"2012","source":"Acta virologica","url":"https://pubmed.ncbi.nlm.nih.gov/23237085","citation_count":7,"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":"8955899","id":"PMC_8955899","title":"Translational coupling in the Escherichia coli operon encoding translation initiation factor IF3 and ribosomal proteins L20 and 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including putative genes for ribosomal protein L35 and a sugar transport protein.","date":"1996","source":"Yeast (Chichester, England)","url":"https://pubmed.ncbi.nlm.nih.gov/8896272","citation_count":2,"is_preprint":false},{"pmid":"39772124","id":"PMC_39772124","title":"A Mutation in the Herpes Simplex Virus Type 1 (HSV-1) UL29 Gene is Associated with Anti-Herpesvirus Drugs' Susceptibility.","date":"2024","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/39772124","citation_count":1,"is_preprint":false},{"pmid":"41065387","id":"PMC_41065387","title":"Ribosomal protein L35 negatively regulates FMDV replication by recruiting AMFR to promote the ubiquitination and degradation of VP2.","date":"2025","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/41065387","citation_count":0,"is_preprint":false},{"pmid":"40847421","id":"PMC_40847421","title":"Escherichia coli proteins uL29 and ACP stabilize the Tn7-encoded TnsD and its DNA 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mapping","url":"https://pubmed.ncbi.nlm.nih.gov/11913794","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":25712,"output_tokens":3554,"usd":0.065223,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11154,"output_tokens":4163,"usd":0.079922,"stage2_stop_reason":"end_turn"},"total_usd":0.145145,"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\": \"RPL35 (L35) was isolated and purified as a component of the 60S large ribosomal subunit from rat liver ribosomes, with molecular weight estimated by SDS-PAGE and amino acid composition 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 purification and characterization, replicated across multiple papers from the same era\",\n      \"pmids\": [\"863909\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"The primary structure of rat ribosomal protein L35 was determined: 122 amino acids (N-terminal methionine removed post-translationally), molecular weight 14,412 Da; the protein is related to archaebacterial L33/L29E and E. coli L29, and contains a possible internal duplication of 11 residues.\",\n      \"method\": \"cDNA sequencing, N-terminal amino acid sequencing, Southern blotting\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct protein sequencing confirmed by cDNA sequence, multiple orthogonal methods\",\n      \"pmids\": [\"2322279\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Human RPL35 carries a 54 aa eukaryotic expansion segment (ES) at the C-terminal end. The first 25 aa of the ES are essential for nuclear import of the protein. The last 29 residues of the ES are not required for ribosome structural or translational functions but serve as a contact site for ribosomal docking to the endoplasmic reticulum.\",\n      \"method\": \"In vivo recombinant ribosome analysis, deletion mutagenesis, subcellular localization assays\",\n      \"journal\": \"Biochemistry and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional mutagenesis with defined phenotypic readouts (nuclear import, ER docking, translation), single lab\",\n      \"pmids\": [\"18523488\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"In yeast (Saccharomyces cerevisiae), depletion of ribosomal protein L35 results in a deficit in 60S ribosomal subunits, half-mer polysomes, and a strong delay in processing of 27SB to 7S pre-rRNAs (cleavage at ITS2 site C2). L35 assembles in the nucleolus and associates with early pre-60S ribosomal particles. Loss of L35 also blocks release of pre-60S particles from nucleolus to nucleoplasm and mildly delays G1 phase of the cell cycle.\",\n      \"method\": \"In vivo depletion, pulse-chase labeling, northern hybridization, primer extension, flow cytometry, deletion mutant analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (pulse-chase, northern, primer extension, flow cytometry) in a single rigorous yeast study establishing specific pre-rRNA processing role\",\n      \"pmids\": [\"20392820\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"RPL35 controls ribosomal translational elongation of β-casein (CSN2) by directly interacting with eukaryotic translational elongation factor 2 (eEF2), with eEF2 acting downstream of RPL35. RPL35 also controls secretion of CSN2 by localizing it to the ER. Methionine promotes RPL35 expression, and RPL35 mediates the methionine signal to regulate CSN2 expression in bovine mammary epithelial cells.\",\n      \"method\": \"Co-immunoprecipitation, colocalization, FRET, gene mutation/overexpression/knockdown\",\n      \"journal\": \"Archives of biochemistry and biophysics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, FRET, and mutagenesis in a single lab, multiple orthogonal methods\",\n      \"pmids\": [\"26297660\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"RPL35 binds the long noncoding RNA lncNB1, and this interaction enhances E2F1 protein synthesis (translational), leading to DEPDC1B gene transcription. DEPDC1B (GTPase-activating protein) then induces ERK phosphorylation and N-Myc protein stabilization. RPL35 knockdown reduces neuroblastoma cell clonogenic capacity.\",\n      \"method\": \"RNA pulldown, Co-IP, loss-of-function (knockdown), reporter assays, in vivo tumor regression\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNA-protein interaction established by pulldown, functional epistasis by knockdown, multiple orthogonal methods in a single lab\",\n      \"pmids\": [\"31690716\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RPL35 knockdown in neuroblastoma cells decreases aerobic glycolysis and increases mitochondrial respiration, decreases HIF1α expression (mRNA and protein), and negatively regulates ERK pathway activity. RPL35 modulates aerobic glycolysis in part through the RPL35/ERK/HIF1α axis.\",\n      \"method\": \"siRNA knockdown, Western blot, metabolic assays (glycolysis/respiration), qPCR\",\n      \"journal\": \"American journal of cancer research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, knockdown with phenotypic readout but pathway placement inferred without epistasis rescue experiments\",\n      \"pmids\": [\"34873488\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RPL35 interacts directly with the Mycoplasma genitalium adhesin protein MgPa (verified by far-Western blot and co-localization), and this interaction promotes expression of EIF2, SRP68, SERBP1, RPL35A, EGF, and TGF-β, and enhances urothelial cell proliferation.\",\n      \"method\": \"T7 phage-display library screening, far-Western blot, co-localization, TMT proteomics, qRT-PCR, MTT assay\",\n      \"journal\": \"Pathogens\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — interaction confirmed by far-Western and co-localization, but downstream mechanism is correlative; single lab\",\n      \"pmids\": [\"34832605\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Drug development study using NMR titration identified that atazanavir and artesunate bind to human RPL35 near the N-terminus; NMR chemical shift mapping revealed the amino acids at the ligand-binding sites, including a binding cluster accessible when RPL35 is integrated into the ribosome.\",\n      \"method\": \"Molecular docking, NMR spectroscopy (chemical shift titration)\",\n      \"journal\": \"Skin pharmacology and physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR with site mapping is a structural method with chemical validation, but functional consequence of binding not confirmed in vivo; single study\",\n      \"pmids\": [\"33823521\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DDX10 interacts with RPL35 (identified by LC-MS/MS and confirmed by Co-IP), and DDX10 is proposed to regulate CRC cell proliferation and metastasis via splicing-related mechanisms involving RPL35.\",\n      \"method\": \"LC-MS/MS, Co-IP\",\n      \"journal\": \"Cancer cell international\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — interaction identified by mass spectrometry and confirmed by single Co-IP, no detailed mechanistic follow-up for RPL35 specifically\",\n      \"pmids\": [\"35109823\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RPL35 protein expression is reduced in chondrocytes under excessive mechanical loading. RPL35 knockdown alone induces chondrocyte senescence, decreases anabolic markers, and increases catabolic markers in part through activation of the Hedgehog (Hh)/Gli1 pathway. Intra-articular overexpression of RPL35 protects against cartilage degeneration in a mouse OA model.\",\n      \"method\": \"RNA sequencing, siRNA knockdown, adenovirus-mediated overexpression, Western blot, immunostaining, in vivo mouse OA model\",\n      \"journal\": \"Journal of orthopaedic translation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined pathway (Hh/Gli1) placement validated in vitro and in vivo, single lab\",\n      \"pmids\": [\"38596341\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TENT5A interacts with RPL35 (Co-IP + GST pull-down confirmed by mass spectrometry) and negatively regulates RPL35 protein stability. The EGR1/TENT5A/RPL35 axis is involved in ribosome biogenesis and negatively regulates the mTOR pathway in hepatocellular carcinoma cells.\",\n      \"method\": \"Co-immunoprecipitation, GST pull-down, mass spectrometry, chromatin immunoprecipitation, dual-luciferase reporter assay, gain/loss-of-function experiments\",\n      \"journal\": \"Cellular oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and GST pulldown confirming interaction, plus functional pathway placement, single lab\",\n      \"pmids\": [\"39570560\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"GADD45GIP1 interacts with RPL35 (identified by IP/LC-MS/MS, ranked second among 263 interacting proteins) and inhibits ubiquitin-mediated proteasomal degradation of RPL35. RPL35 knockdown activates the PERK-eIF2α ER stress pathway, increases ER stress, and reduces osteosarcoma cell viability. Overexpression of RPL35 counteracts the decrease in cell viability caused by GADD45GIP1 knockdown.\",\n      \"method\": \"Immunoprecipitation, LC-MS/MS, siRNA knockdown, overexpression rescue, Western blot for ubiquitination/PERK/eIF2α\",\n      \"journal\": \"Cancer cell international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — IP/MS-confirmed interaction, epistasis rescue experiment, ubiquitination measurement, single lab\",\n      \"pmids\": [\"40604925\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RPL35 functions as an antiviral host protein against FMDV by directly interacting with the FMDV structural protein VP2 and recruiting the E3 ubiquitin ligase AMFR to mediate K48-linked polyubiquitination and proteasomal degradation of VP2. The Lys217 residue of VP2 is critical for this RPL35-mediated antiviral activity. FMDV counteracts this by inducing degradation of KPNA3, thereby blocking RPL35 nuclear translocation.\",\n      \"method\": \"Co-IP, proteomic screen, ubiquitination assay, site-directed mutagenesis (VP2-K217R recombinant virus), KPNA3 knockdown/degradation assay\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — interaction and ubiquitination confirmed by Co-IP and mutant virus, multiple orthogonal methods in single study; not yet independently replicated\",\n      \"pmids\": [\"41065387\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RPL35 (uL29/L35) is a structural component of the 60S ribosomal large subunit required for 27SB pre-rRNA processing and early pre-60S particle biogenesis; its eukaryotic C-terminal expansion segment mediates nuclear import (first 25 aa) and ER docking (last 29 aa), while its interaction with eEF2 controls translational elongation. Beyond its ribosomal role, RPL35 participates in extra-ribosomal functions: it binds lncNB1 to enhance E2F1 translation and N-Myc stabilization via ERK, recruits AMFR E3 ligase to ubiquitinate and degrade the FMDV capsid protein VP2 (antiviral), is stabilized by GADD45GIP1 to modulate ER stress via PERK/eIF2α, and is regulated in chondrocytes through the Hedgehog/Gli1 pathway; its protein stability is also regulated by TENT5A-dependent mechanisms in the EGR1/TENT5A/RPL35/mTOR axis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPL35 (uL29/L35) is a structural protein of the 60S large ribosomal subunit that is also required for early large-subunit biogenesis [#0, #3]. First purified from rat liver ribosomes and sequenced as a 122-residue protein related to archaebacterial L33/L29E and E. coli L29 [#0, #1], it assembles in the nucleolus on early pre-60S particles, and its depletion in yeast causes a deficit of 60S subunits, a strong delay in 27SB-to-7S pre-rRNA processing at ITS2 site C2, and a block in pre-60S nucleolus-to-nucleoplasm release [#3]. In eukaryotes the protein carries a 54-aa C-terminal expansion segment whose first 25 residues are essential for nuclear import while its last 29 residues mediate ribosome docking to the endoplasmic reticulum [#2]. RPL35 directly binds elongation factor eEF2 to control translational elongation and ER-localized secretion of nascent protein [#4]. Beyond the ribosome, RPL35 has acquired extra-ribosomal regulatory roles: it binds the lncRNA lncNB1 to enhance E2F1 translation and drive a DEPDC1B–ERK–N-Myc axis supporting neuroblastoma proliferation [#5], it acts as an antiviral host factor that recruits the E3 ligase AMFR to mediate K48-linked polyubiquitination and proteasomal degradation of the FMDV capsid protein VP2 [#13], and its own stability is set by competing factors—negatively by TENT5A within an EGR1/TENT5A/RPL35/mTOR axis [#11] and positively by GADD45GIP1, which blocks ubiquitin-mediated degradation of RPL35 and thereby restrains the PERK–eIF2\\u03b1 ER stress pathway [#12]. RPL35 also protects chondrocytes against senescence and cartilage degeneration via suppression of the Hedgehog/Gli1 pathway [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 1977,\n      \"claim\": \"Established that L35 is a discrete, purifiable protein component of the eukaryotic 60S large ribosomal subunit, defining the molecule biochemically.\",\n      \"evidence\": \"Ion-exchange/gel-filtration purification, SDS-PAGE and amino acid composition from rat liver ribosomes\",\n      \"pmids\": [\"863909\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No sequence or structural position within the subunit\", \"No functional role assigned\"]\n    },\n    {\n      \"year\": 1990,\n      \"claim\": \"Resolved the primary structure and evolutionary relationships of the protein, placing it in the L29/L33E family and revealing an internal sequence duplication.\",\n      \"evidence\": \"cDNA and N-terminal protein sequencing with Southern blotting\",\n      \"pmids\": [\"2322279\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional significance of the internal duplication unknown\", \"No mechanistic role established\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Showed that the eukaryote-specific C-terminal expansion segment partitions distinct trafficking functions—nuclear import versus ER docking—separable from core ribosomal/translational function.\",\n      \"evidence\": \"Recombinant ribosome analysis with deletion mutagenesis and subcellular localization assays\",\n      \"pmids\": [\"18523488\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Import receptor not identified here\", \"Single lab; structural basis of ER docking not resolved\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defined the precise biogenesis role: L35 assembles in the nucleolus on early pre-60S particles and is required for 27SB pre-rRNA processing and pre-60S nuclear export.\",\n      \"evidence\": \"Yeast depletion with pulse-chase, northern, primer extension and flow cytometry\",\n      \"pmids\": [\"20392820\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct interaction partners on pre-60S not mapped\", \"Human ortholog biogenesis role inferred from yeast\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Connected RPL35 to the elongation machinery and secretory output by demonstrating a direct eEF2 interaction controlling elongation and ER targeting of a secreted protein.\",\n      \"evidence\": \"Reciprocal Co-IP, FRET, colocalization and mutagenesis/knockdown in bovine mammary epithelial cells\",\n      \"pmids\": [\"26297660\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Generality beyond CSN2 substrate not tested\", \"Mechanism of methionine-dependent regulation unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Revealed an extra-ribosomal, RNA-binding function in which RPL35 partners with lncNB1 to selectively enhance E2F1 translation and drive an oncogenic ERK/N-Myc cascade.\",\n      \"evidence\": \"RNA pulldown, Co-IP, knockdown, reporter assays and in vivo tumor regression in neuroblastoma\",\n      \"pmids\": [\"31690716\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether translational selectivity is ribosome-dependent unclear\", \"Direct lncNB1-binding region of RPL35 not mapped\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended the neuroblastoma role to metabolic control, placing RPL35 upstream of an ERK/HIF1\\u03b1 axis governing aerobic glycolysis.\",\n      \"evidence\": \"siRNA knockdown with metabolic assays, Western blot and qPCR\",\n      \"pmids\": [\"34873488\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Pathway placement inferred without epistasis rescue\", \"Single lab, correlative\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Implicated RPL35 as a host target of a bacterial adhesin, linking the protein to proliferative signaling during Mycoplasma infection.\",\n      \"evidence\": \"Phage display, far-Western, colocalization, TMT proteomics and MTT in urothelial cells\",\n      \"pmids\": [\"34832605\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Downstream effects correlative\", \"No reciprocal validation of functional consequence\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Provided structural ligand-binding information by mapping small-molecule (atazanavir, artesunate) contact sites on human RPL35.\",\n      \"evidence\": \"Molecular docking and NMR chemical-shift titration\",\n      \"pmids\": [\"33823521\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of binding not tested in vivo\", \"Single study\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified DDX10 as a physical interactor of RPL35 in colorectal cancer, hinting at a link between RPL35 and splicing-associated processes.\",\n      \"evidence\": \"LC-MS/MS and Co-IP\",\n      \"pmids\": [\"35109823\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mechanistic follow-up for RPL35 specifically\", \"Single Co-IP without reciprocal validation\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established a protective role for RPL35 in chondrocyte homeostasis, where its loss promotes senescence via Hedgehog/Gli1 activation and its restoration limits OA cartilage degeneration.\",\n      \"evidence\": \"RNA-seq, siRNA knockdown, adenoviral overexpression and an in vivo mouse OA model\",\n      \"pmids\": [\"38596341\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking RPL35 to Hh/Gli1 not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined RPL35 as a regulated node whose stability is negatively controlled by TENT5A within an EGR1/TENT5A/RPL35 axis that restrains mTOR signaling in hepatocellular carcinoma.\",\n      \"evidence\": \"Co-IP, GST pull-down, mass spectrometry, ChIP and luciferase reporter with gain/loss-of-function\",\n      \"pmids\": [\"39570560\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of TENT5A-mediated destabilization unclear\", \"Direct link of RPL35 to mTOR not resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed RPL35 protein abundance is set by ubiquitin-mediated turnover that GADD45GIP1 antagonizes, coupling RPL35 stability to control of the PERK-eIF2\\u03b1 ER stress response.\",\n      \"evidence\": \"IP/LC-MS/MS, siRNA knockdown, overexpression rescue and ubiquitination/PERK/eIF2\\u03b1 Western blots in osteosarcoma\",\n      \"pmids\": [\"40604925\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ligase for RPL35 in this context not identified\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated an antiviral effector function: RPL35 recruits AMFR to ubiquitinate and degrade the FMDV capsid protein VP2, a defense the virus evades by blocking RPL35 nuclear translocation.\",\n      \"evidence\": \"Co-IP, proteomic screen, ubiquitination assay, VP2-K217R recombinant virus and KPNA3 degradation assay\",\n      \"pmids\": [\"41065387\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether antiviral activity is ribosome-independent unclear\", \"Not independently replicated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RPL35's core ribosomal function is mechanistically partitioned from its diverse extra-ribosomal roles—and what governs its differential engagement across these contexts—remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model integrating ribosomal and extra-ribosomal interfaces\", \"Direct RNA- and protein-binding surfaces for extra-ribosomal partners unmapped\", \"No human Mendelian disease link established in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 13]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [2, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\"60S large ribosomal subunit\", \"pre-60S ribosomal particle\"],\n    \"partners\": [\"EEF2\", \"lncNB1\", \"AMFR\", \"TENT5A\", \"GADD45GIP1\", \"DDX10\", \"KPNA3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}