{"gene":"MRPL35","run_date":"2026-06-10T02:59:51","timeline":{"discoveries":[{"year":2017,"finding":"MrpL35 (mL38) assembles into a subcomplex with MrpL7 (uL5), Mrp7 (bL27), MrpL36 (bL31), MrpL17 (mL46), and MrpL28 (mL40) within the mitoribosomal central protuberance in yeast.","method":"Biochemical subcomplex isolation / co-purification in yeast mitochondria","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical subcomplex isolation with multiple partner proteins, single lab, single study","pmids":["28931599"],"is_preprint":false},{"year":2017,"finding":"MrpL35 and its partner Mrp7 coordinate Cox1 synthesis with its assembly into cytochrome c oxidase (COX), functioning through the COX assembly factors Cox14 and Coa3; loss-of-function mrpL35 mutants show a COX assembly defect without a general block in mitochondrial protein synthesis.","method":"Genetic analysis of respiratory-defective mrpL35 mutant yeast; analysis of mitochondrial translation products and COX assembly intermediates","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean loss-of-function yeast genetics with defined COX assembly phenotype distinguishable from general translation inhibition, single lab","pmids":["28931599"],"is_preprint":false},{"year":2023,"finding":"Mutation of the PEBP-invariant ligand-binding residues Asp232 and Arg288 in the PEBP-homology domain of MrpL35/mL38, as well as Asp167 of MrpL35 and Arg127 of neighboring Mrp7/bL27m, impairs OXPHOS complex assembly without inhibiting mitochondrial translation, indicating these charged residues form a functionally important microenvironment that ensures newly synthesized proteins are competent for OXPHOS assembly.","method":"Site-directed mutagenesis of PEBP-domain residues in yeast; measurement of OXPHOS complex levels and mitochondrial translation rates","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1 / Moderate — active-site mutagenesis with functional validation distinguishing translation from assembly competency, single lab but multiple mutants and orthogonal readouts","pmids":["37792492"],"is_preprint":false},{"year":2025,"finding":"During late-stage yeast mitoribosome large subunit biogenesis, MrpL35 (bL35m) incorporation depends on Mtg1-mediated restructuring of 21S rRNA helices H73-75 and H93 and subsequent peptidyl transfer center region maturation; bL35m is incorporated coordinately with uL6m, uL16m, and bL36m during this late assembly step.","method":"Cryo-EM structures of mtLSU assembly intermediates; genetic depletion of assembly factors (Mtg1, Mrh4, uL16m); in vitro reconstitution approaches","journal":"Biochimica et biophysica acta. Molecular cell research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structural data combined with genetic depletion and in vitro reconstitution establishing ordered assembly hierarchy, single study","pmids":["40865570"],"is_preprint":false},{"year":2024,"finding":"USP39 stabilizes MRPL35 protein expression in NSCLC cells through deubiquitination, preventing its proteasomal degradation; MRPL35 in turn positively regulates SLC7A5 expression to promote glutamine metabolism, and the pro-tumorigenic effects of MRPL35 are rescued by SLC7A5 overexpression when MRPL35 is silenced.","method":"Cellular ubiquitination assay; knockdown/overexpression experiments; glutamine consumption, α-ketoglutarate, and glutamate production assays; in vivo xenograft","journal":"The clinical respiratory journal","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — deubiquitination assay and epistasis rescue experiment, single lab, single study","pmids":["38987867"],"is_preprint":false},{"year":2019,"finding":"MRPL35 knockdown in colorectal cancer cells increases reactive oxygen species (ROS) production, induces DNA damage, G2/M arrest, loss of mitochondrial membrane potential, apoptosis, and autophagy; ROS scavenger N-acetylcysteine or MRPL35 overexpression abrogates these effects, placing MRPL35 upstream of ROS in this pathway.","method":"siRNA knockdown; ROS measurement; flow cytometry for cell cycle and apoptosis; mitochondrial membrane potential assay; xenograft mouse model; rescue with NAC or MRPL35 overexpression","journal":"The American journal of pathology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal cellular assays with genetic rescue and ROS scavenger rescue, single lab","pmids":["30862482"],"is_preprint":false},{"year":2021,"finding":"Knockdown of MRPL35 in gastric carcinoma cells decreases PICK1 and BCL-XL protein expression and increases AGR2, identifying these as downstream effectors of MRPL35 in cell proliferation and survival.","method":"shRNA knockdown; isobaric tags for relative and absolute quantification (iTRAQ) proteomics; Western blot validation; xenograft nude mouse model","journal":"World journal of gastroenterology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — iTRAQ proteomics plus Western blot downstream target identification after knockdown, single lab","pmids":["33967557"],"is_preprint":false},{"year":2023,"finding":"Knockdown of MRPL35 in NSCLC cells activates the p53 signaling pathway and reduces expression of cell cycle regulators CDK1, BIRC5, CHEK1, STMN1, and MCM2, indicating MRPL35 sustains cell cycle progression by suppressing p53 and maintaining these downstream cell cycle genes.","method":"Lentiviral shRNA knockdown; Western blot for pathway proteins; colony formation assay; in vivo xenograft imaging","journal":"BMC pulmonary medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — knockdown with defined downstream protein readouts by Western blot, single lab, single study","pmids":["38093266"],"is_preprint":false},{"year":2023,"finding":"The lncRNA ADPGK-AS1, partly localized in mitochondria, directly binds MRPL35; ADPGK-AS1 overexpression upregulates TCA cycle activity and promotes mitochondrial fission, suggesting MRPL35 is engaged by this lncRNA to modulate macrophage metabolic state.","method":"RNA-protein binding assay (lncRNA-MRPL35 interaction); metabolic profiling; macrophage knockdown/overexpression in vitro and in vivo","journal":"The EMBO journal","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single binding interaction reported in abstract without detailed mechanistic follow-up specifically on MRPL35's contribution, single lab","pmids":["37545364"],"is_preprint":false},{"year":2025,"finding":"MRPL35 overexpression in a rat parenteral nutrition-associated cholestasis (PNAC) model reduces JNK and NF-κB pathway activation, inflammatory cytokines, oxidative stress (ROS), and hepatocyte apoptosis, placing MRPL35 upstream of the ROS/JNK/NF-κB axis in hepatic inflammation.","method":"Adenovirus-mediated MRPL35 overexpression in rat PNAC model; ELISA, immunohistochemistry, Western blotting for pathway proteins; NAC co-treatment as mechanistic control","journal":"Journal of inflammation research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — in vivo gain-of-function with pathway protein readouts and pharmacological rescue, single lab, single study","pmids":["41049074"],"is_preprint":false}],"current_model":"MRPL35 (bL35m/mL38) is a mitospecific component of the mitoribosomal central protuberance whose PEBP-homology domain, together with partner protein Mrp7/bL27m, forms a regulatory region that coordinates mitochondrial translation with OXPHOS complex assembly—particularly cytochrome c oxidase biogenesis via Cox14 and Coa3—without acting as a general translational subunit; its incorporation during late large-subunit maturation is ordered downstream of Mtg1-directed rRNA refolding, and in mammalian cancer contexts it is stabilized by USP39-mediated deubiquitination and sustains cell proliferation by suppressing ROS production and p53 signaling while promoting SLC7A5-dependent glutamine metabolism."},"narrative":{"mechanistic_narrative":"MRPL35 (bL35m/mL38) is a mitospecific component of the mitochondrial ribosome large subunit, assembling into a subcomplex of the central protuberance together with partner proteins including Mrp7/bL27m [PMID:28931599]. Rather than acting as a general translational subunit, it couples the synthesis of mitochondrially encoded OXPHOS subunits to their assembly: loss-of-function mrpL35 mutants display a cytochrome c oxidase assembly defect, mediated through the COX assembly factors Cox14 and Coa3, without a general block in mitochondrial protein synthesis [PMID:28931599]. This assembly-coupling function localizes to a PEBP-homology domain, where invariant charged ligand-binding residues (Asp232, Arg288, Asp167) together with Arg127 of the neighboring Mrp7/bL27m form a microenvironment that renders newly synthesized proteins competent for OXPHOS assembly; mutating these residues impairs OXPHOS assembly while leaving translation intact [PMID:37792492]. MRPL35 is incorporated during late large-subunit biogenesis, downstream of Mtg1-mediated restructuring of 21S rRNA helices and peptidyl transfer center maturation, coordinately with uL6m, uL16m, and bL36m [PMID:40865570]. In mammalian cancer contexts, MRPL35 sustains proliferation and survival: its knockdown elevates ROS, inducing DNA damage, cell cycle arrest, and apoptosis [PMID:30862482], and it suppresses p53 signaling while maintaining cell cycle regulators [PMID:38093266]. Its protein levels are stabilized by USP39-mediated deubiquitination, and it promotes SLC7A5-dependent glutamine metabolism [PMID:38987867].","teleology":[{"year":2017,"claim":"Establishing where MRPL35 physically sits in the mitoribosome and what it does there distinguished it from a generic ribosomal subunit, revealing a role in coupling translation to OXPHOS assembly.","evidence":"Biochemical subcomplex isolation in yeast mitochondria plus genetic analysis of respiratory-defective mrpL35 mutants and COX assembly intermediates","pmids":["28931599"],"confidence":"Medium","gaps":["Mechanism by which the bL35m/Mrp7 subcomplex communicates with Cox14/Coa3 not resolved","Single lab","Not validated in mammalian mitoribosome"]},{"year":2023,"claim":"Pinpointing the PEBP-homology domain charged residues showed the assembly-coupling activity is a discrete functional microenvironment separable from translation.","evidence":"Site-directed mutagenesis of PEBP-domain residues in yeast with parallel OXPHOS complex and translation rate readouts","pmids":["37792492"],"confidence":"High","gaps":["Identity of any ligand bound by the PEBP pocket unknown","Structural mechanism of how the microenvironment confers assembly competency unresolved"]},{"year":2025,"claim":"Defining the assembly hierarchy placed MRPL35 incorporation at a specific late step of large-subunit maturation downstream of rRNA refolding, clarifying biogenesis order.","evidence":"Cryo-EM of mtLSU assembly intermediates with genetic depletion of assembly factors and in vitro reconstitution in yeast","pmids":["40865570"],"confidence":"High","gaps":["What triggers coordinate incorporation of bL35m with uL6m/uL16m/bL36m not defined","Mammalian assembly order not directly addressed"]},{"year":2019,"claim":"Linking MRPL35 to ROS suppression in cancer cells established a pro-survival mitochondrial role beyond ribosome structure.","evidence":"siRNA knockdown in colorectal cancer cells with ROS, cell cycle, apoptosis, and membrane potential assays, plus NAC and overexpression rescue and xenograft","pmids":["30862482"],"confidence":"Medium","gaps":["Molecular link between MRPL35 loss and ROS rise not mechanistically defined","Relationship to its mitoribosomal assembly function unexplored"]},{"year":2021,"claim":"Proteomic profiling after knockdown nominated downstream effectors of MRPL35 in proliferation and survival.","evidence":"shRNA knockdown with iTRAQ proteomics and Western validation in gastric carcinoma cells plus xenograft","pmids":["33967557"],"confidence":"Medium","gaps":["Whether PICK1/BCL-XL/AGR2 changes are direct or secondary unknown","No mechanistic connection to mitoribosome function"]},{"year":2023,"claim":"Connecting MRPL35 to p53 suppression and cell cycle gene maintenance defined a transcriptional/signaling axis sustaining proliferation.","evidence":"Lentiviral shRNA knockdown in NSCLC cells with Western blot pathway readouts, colony formation, and xenograft imaging","pmids":["38093266"],"confidence":"Medium","gaps":["How a mitoribosomal protein represses p53 signaling not established","Direct vs indirect regulation of cell cycle genes unresolved"]},{"year":2023,"claim":"Identifying a direct lncRNA partner raised the possibility of post-translational regulation of mitochondrial metabolic state via MRPL35.","evidence":"RNA-protein binding assay and metabolic profiling in macrophages in vitro and in vivo","pmids":["37545364"],"confidence":"Low","gaps":["Single binding interaction reported without detailed mechanistic follow-up on MRPL35's specific contribution","Functional consequence of the lncRNA-MRPL35 interaction not isolated"]},{"year":2024,"claim":"Defining USP39-mediated stabilization and the SLC7A5/glutamine link placed MRPL35 in a deubiquitination-controlled metabolic circuit in cancer.","evidence":"Cellular ubiquitination assay, knockdown/overexpression, glutamine metabolism assays, and epistasis rescue with SLC7A5 in NSCLC cells plus xenograft","pmids":["38987867"],"confidence":"Medium","gaps":["Mechanism by which MRPL35 regulates SLC7A5 expression unknown","Whether stabilization affects mitoribosomal vs metabolic functions not separated"]},{"year":2025,"claim":"Gain-of-function in a cholestasis model extended the ROS-suppressing role of MRPL35 to control of hepatic inflammatory signaling.","evidence":"Adenovirus-mediated MRPL35 overexpression in a rat PNAC model with pathway protein readouts and NAC mechanistic control","pmids":["41049074"],"confidence":"Medium","gaps":["Whether the anti-inflammatory effect derives from mitoribosomal function unclear","Upstream determinants of MRPL35 levels in this context undefined"]},{"year":null,"claim":"How the conserved mitoribosomal assembly-coupling function of MRPL35 mechanistically connects to its ROS-, p53-, and metabolism-modulating roles in mammalian cells remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No study bridges the yeast structural/assembly mechanism with the mammalian cancer signaling phenotypes","Endogenous ligand of the PEBP domain unidentified","Direct molecular targets in p53 and SLC7A5 regulation not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,3]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[8]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[0,3]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[3]}],"complexes":["mitochondrial ribosome large subunit","mitoribosomal central protuberance"],"partners":["MRP7","MRPL7","MRPL36","MRPL17","MRPL28","USP39","ADPGK-AS1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NZE8","full_name":"Large ribosomal subunit protein bL35m","aliases":["39S ribosomal protein L35, mitochondrial","L35mt","MRP-L35"],"length_aa":188,"mass_kda":21.5,"function":"","subcellular_location":"Mitochondrion","url":"https://www.uniprot.org/uniprotkb/Q9NZE8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/MRPL35","classification":"Common Essential","n_dependent_lines":898,"n_total_lines":1208,"dependency_fraction":0.7433774834437086},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/MRPL35","total_profiled":1310},"omim":[{"mim_id":"611841","title":"MITOCHONDRIAL RIBOSOMAL PROTEIN L35; MRPL35","url":"https://www.omim.org/entry/611841"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/MRPL35"},"hgnc":{"alias_symbol":["bL35m"],"prev_symbol":[]},"alphafold":{"accession":"Q9NZE8","domains":[{"cath_id":"4.10.410","chopping":"109-167","consensus_level":"high","plddt":97.2383,"start":109,"end":167}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NZE8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NZE8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NZE8-F1-predicted_aligned_error_v6.png","plddt_mean":74.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MRPL35","jax_strain_url":"https://www.jax.org/strain/search?query=MRPL35"},"sequence":{"accession":"Q9NZE8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NZE8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NZE8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NZE8"}},"corpus_meta":[{"pmid":"28931599","id":"PMC_28931599","title":"MrpL35, a mitospecific component of mitoribosomes, plays a key role in cytochrome c oxidase assembly.","date":"2017","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/28931599","citation_count":32,"is_preprint":false},{"pmid":"30862482","id":"PMC_30862482","title":"MRPL35 Is Up-Regulated in Colorectal Cancer and Regulates Colorectal Cancer Cell Growth and Apoptosis.","date":"2019","source":"The American journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/30862482","citation_count":28,"is_preprint":false},{"pmid":"37545364","id":"PMC_37545364","title":"ADPGK-AS1 long noncoding RNA switches macrophage metabolic and phenotypic state to promote lung cancer growth.","date":"2023","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/37545364","citation_count":27,"is_preprint":false},{"pmid":"35979263","id":"PMC_35979263","title":"18β-glycyrrhetinic acid regulates mitochondrial ribosomal protein L35-associated apoptosis signaling pathways to inhibit proliferation of gastric carcinoma cells.","date":"2022","source":"World journal of gastroenterology","url":"https://pubmed.ncbi.nlm.nih.gov/35979263","citation_count":19,"is_preprint":false},{"pmid":"38987867","id":"PMC_38987867","title":"MRPL35 Induces Proliferation, Invasion, and Glutamine Metabolism in NSCLC Cells by Upregulating SLC7A5 Expression.","date":"2024","source":"The clinical respiratory journal","url":"https://pubmed.ncbi.nlm.nih.gov/38987867","citation_count":10,"is_preprint":false},{"pmid":"33967557","id":"PMC_33967557","title":"Depletion of MRPL35 inhibits gastric carcinoma cell proliferation by regulating downstream signaling proteins.","date":"2021","source":"World journal of gastroenterology","url":"https://pubmed.ncbi.nlm.nih.gov/33967557","citation_count":9,"is_preprint":false},{"pmid":"32655625","id":"PMC_32655625","title":"Genome Regulation and Gene Interaction Networks Inferred From Muscle Transcriptome Underlying Feed Efficiency in Pigs.","date":"2020","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32655625","citation_count":8,"is_preprint":false},{"pmid":"38093266","id":"PMC_38093266","title":"Knockdown of MRPL35 promotes cell apoptosis and inhibits cell proliferation in non-small-cell lung cancer.","date":"2023","source":"BMC pulmonary medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38093266","citation_count":7,"is_preprint":false},{"pmid":"37736554","id":"PMC_37736554","title":"Identification and validation of a fatty acid metabolism gene signature for the promotion of metastasis in liver cancer.","date":"2023","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/37736554","citation_count":5,"is_preprint":false},{"pmid":"37792492","id":"PMC_37792492","title":"Mutation of the PEBP-like domain of the mitoribosomal MrpL35/mL38 protein results in production of nascent chains with impaired capacity to assemble into OXPHOS complexes.","date":"2023","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/37792492","citation_count":4,"is_preprint":false},{"pmid":"41049074","id":"PMC_41049074","title":"MRPL35 Attenuates Neonatal Parenteral Nutrition-Associated Cholestasis by Modulating the ROS/JNK/NF-κB Pathway.","date":"2025","source":"Journal of inflammation research","url":"https://pubmed.ncbi.nlm.nih.gov/41049074","citation_count":0,"is_preprint":false},{"pmid":"40865570","id":"PMC_40865570","title":"The late stages of yeast mitoribosome large subunit biogenesis.","date":"2025","source":"Biochimica et biophysica acta. Molecular cell research","url":"https://pubmed.ncbi.nlm.nih.gov/40865570","citation_count":0,"is_preprint":false},{"pmid":"41889637","id":"PMC_41889637","title":"Integrated expression quantitative trait loci and Mendelian randomization analyses of the candidate genes and pathways identified for myocardial infarction.","date":"2026","source":"Frontiers in molecular biosciences","url":"https://pubmed.ncbi.nlm.nih.gov/41889637","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9789,"output_tokens":2575,"usd":0.033996,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9794,"output_tokens":3229,"usd":0.064848,"stage2_stop_reason":"end_turn"},"total_usd":0.098844,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"MrpL35 (mL38) assembles into a subcomplex with MrpL7 (uL5), Mrp7 (bL27), MrpL36 (bL31), MrpL17 (mL46), and MrpL28 (mL40) within the mitoribosomal central protuberance in yeast.\",\n      \"method\": \"Biochemical subcomplex isolation / co-purification in yeast mitochondria\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical subcomplex isolation with multiple partner proteins, single lab, single study\",\n      \"pmids\": [\"28931599\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"MrpL35 and its partner Mrp7 coordinate Cox1 synthesis with its assembly into cytochrome c oxidase (COX), functioning through the COX assembly factors Cox14 and Coa3; loss-of-function mrpL35 mutants show a COX assembly defect without a general block in mitochondrial protein synthesis.\",\n      \"method\": \"Genetic analysis of respiratory-defective mrpL35 mutant yeast; analysis of mitochondrial translation products and COX assembly intermediates\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean loss-of-function yeast genetics with defined COX assembly phenotype distinguishable from general translation inhibition, single lab\",\n      \"pmids\": [\"28931599\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Mutation of the PEBP-invariant ligand-binding residues Asp232 and Arg288 in the PEBP-homology domain of MrpL35/mL38, as well as Asp167 of MrpL35 and Arg127 of neighboring Mrp7/bL27m, impairs OXPHOS complex assembly without inhibiting mitochondrial translation, indicating these charged residues form a functionally important microenvironment that ensures newly synthesized proteins are competent for OXPHOS assembly.\",\n      \"method\": \"Site-directed mutagenesis of PEBP-domain residues in yeast; measurement of OXPHOS complex levels and mitochondrial translation rates\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — active-site mutagenesis with functional validation distinguishing translation from assembly competency, single lab but multiple mutants and orthogonal readouts\",\n      \"pmids\": [\"37792492\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"During late-stage yeast mitoribosome large subunit biogenesis, MrpL35 (bL35m) incorporation depends on Mtg1-mediated restructuring of 21S rRNA helices H73-75 and H93 and subsequent peptidyl transfer center region maturation; bL35m is incorporated coordinately with uL6m, uL16m, and bL36m during this late assembly step.\",\n      \"method\": \"Cryo-EM structures of mtLSU assembly intermediates; genetic depletion of assembly factors (Mtg1, Mrh4, uL16m); in vitro reconstitution approaches\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structural data combined with genetic depletion and in vitro reconstitution establishing ordered assembly hierarchy, single study\",\n      \"pmids\": [\"40865570\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"USP39 stabilizes MRPL35 protein expression in NSCLC cells through deubiquitination, preventing its proteasomal degradation; MRPL35 in turn positively regulates SLC7A5 expression to promote glutamine metabolism, and the pro-tumorigenic effects of MRPL35 are rescued by SLC7A5 overexpression when MRPL35 is silenced.\",\n      \"method\": \"Cellular ubiquitination assay; knockdown/overexpression experiments; glutamine consumption, α-ketoglutarate, and glutamate production assays; in vivo xenograft\",\n      \"journal\": \"The clinical respiratory journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — deubiquitination assay and epistasis rescue experiment, single lab, single study\",\n      \"pmids\": [\"38987867\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"MRPL35 knockdown in colorectal cancer cells increases reactive oxygen species (ROS) production, induces DNA damage, G2/M arrest, loss of mitochondrial membrane potential, apoptosis, and autophagy; ROS scavenger N-acetylcysteine or MRPL35 overexpression abrogates these effects, placing MRPL35 upstream of ROS in this pathway.\",\n      \"method\": \"siRNA knockdown; ROS measurement; flow cytometry for cell cycle and apoptosis; mitochondrial membrane potential assay; xenograft mouse model; rescue with NAC or MRPL35 overexpression\",\n      \"journal\": \"The American journal of pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal cellular assays with genetic rescue and ROS scavenger rescue, single lab\",\n      \"pmids\": [\"30862482\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Knockdown of MRPL35 in gastric carcinoma cells decreases PICK1 and BCL-XL protein expression and increases AGR2, identifying these as downstream effectors of MRPL35 in cell proliferation and survival.\",\n      \"method\": \"shRNA knockdown; isobaric tags for relative and absolute quantification (iTRAQ) proteomics; Western blot validation; xenograft nude mouse model\",\n      \"journal\": \"World journal of gastroenterology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — iTRAQ proteomics plus Western blot downstream target identification after knockdown, single lab\",\n      \"pmids\": [\"33967557\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Knockdown of MRPL35 in NSCLC cells activates the p53 signaling pathway and reduces expression of cell cycle regulators CDK1, BIRC5, CHEK1, STMN1, and MCM2, indicating MRPL35 sustains cell cycle progression by suppressing p53 and maintaining these downstream cell cycle genes.\",\n      \"method\": \"Lentiviral shRNA knockdown; Western blot for pathway proteins; colony formation assay; in vivo xenograft imaging\",\n      \"journal\": \"BMC pulmonary medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — knockdown with defined downstream protein readouts by Western blot, single lab, single study\",\n      \"pmids\": [\"38093266\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The lncRNA ADPGK-AS1, partly localized in mitochondria, directly binds MRPL35; ADPGK-AS1 overexpression upregulates TCA cycle activity and promotes mitochondrial fission, suggesting MRPL35 is engaged by this lncRNA to modulate macrophage metabolic state.\",\n      \"method\": \"RNA-protein binding assay (lncRNA-MRPL35 interaction); metabolic profiling; macrophage knockdown/overexpression in vitro and in vivo\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single binding interaction reported in abstract without detailed mechanistic follow-up specifically on MRPL35's contribution, single lab\",\n      \"pmids\": [\"37545364\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"MRPL35 overexpression in a rat parenteral nutrition-associated cholestasis (PNAC) model reduces JNK and NF-κB pathway activation, inflammatory cytokines, oxidative stress (ROS), and hepatocyte apoptosis, placing MRPL35 upstream of the ROS/JNK/NF-κB axis in hepatic inflammation.\",\n      \"method\": \"Adenovirus-mediated MRPL35 overexpression in rat PNAC model; ELISA, immunohistochemistry, Western blotting for pathway proteins; NAC co-treatment as mechanistic control\",\n      \"journal\": \"Journal of inflammation research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — in vivo gain-of-function with pathway protein readouts and pharmacological rescue, single lab, single study\",\n      \"pmids\": [\"41049074\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MRPL35 (bL35m/mL38) is a mitospecific component of the mitoribosomal central protuberance whose PEBP-homology domain, together with partner protein Mrp7/bL27m, forms a regulatory region that coordinates mitochondrial translation with OXPHOS complex assembly—particularly cytochrome c oxidase biogenesis via Cox14 and Coa3—without acting as a general translational subunit; its incorporation during late large-subunit maturation is ordered downstream of Mtg1-directed rRNA refolding, and in mammalian cancer contexts it is stabilized by USP39-mediated deubiquitination and sustains cell proliferation by suppressing ROS production and p53 signaling while promoting SLC7A5-dependent glutamine metabolism.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"MRPL35 (bL35m/mL38) is a mitospecific component of the mitochondrial ribosome large subunit, assembling into a subcomplex of the central protuberance together with partner proteins including Mrp7/bL27m [#0]. Rather than acting as a general translational subunit, it couples the synthesis of mitochondrially encoded OXPHOS subunits to their assembly: loss-of-function mrpL35 mutants display a cytochrome c oxidase assembly defect, mediated through the COX assembly factors Cox14 and Coa3, without a general block in mitochondrial protein synthesis [#1]. This assembly-coupling function localizes to a PEBP-homology domain, where invariant charged ligand-binding residues (Asp232, Arg288, Asp167) together with Arg127 of the neighboring Mrp7/bL27m form a microenvironment that renders newly synthesized proteins competent for OXPHOS assembly; mutating these residues impairs OXPHOS assembly while leaving translation intact [#2]. MRPL35 is incorporated during late large-subunit biogenesis, downstream of Mtg1-mediated restructuring of 21S rRNA helices and peptidyl transfer center maturation, coordinately with uL6m, uL16m, and bL36m [#3]. In mammalian cancer contexts, MRPL35 sustains proliferation and survival: its knockdown elevates ROS, inducing DNA damage, cell cycle arrest, and apoptosis [#5], and it suppresses p53 signaling while maintaining cell cycle regulators [#7]. Its protein levels are stabilized by USP39-mediated deubiquitination, and it promotes SLC7A5-dependent glutamine metabolism [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Establishing where MRPL35 physically sits in the mitoribosome and what it does there distinguished it from a generic ribosomal subunit, revealing a role in coupling translation to OXPHOS assembly.\",\n      \"evidence\": \"Biochemical subcomplex isolation in yeast mitochondria plus genetic analysis of respiratory-defective mrpL35 mutants and COX assembly intermediates\",\n      \"pmids\": [\"28931599\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which the bL35m/Mrp7 subcomplex communicates with Cox14/Coa3 not resolved\", \"Single lab\", \"Not validated in mammalian mitoribosome\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Pinpointing the PEBP-homology domain charged residues showed the assembly-coupling activity is a discrete functional microenvironment separable from translation.\",\n      \"evidence\": \"Site-directed mutagenesis of PEBP-domain residues in yeast with parallel OXPHOS complex and translation rate readouts\",\n      \"pmids\": [\"37792492\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of any ligand bound by the PEBP pocket unknown\", \"Structural mechanism of how the microenvironment confers assembly competency unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defining the assembly hierarchy placed MRPL35 incorporation at a specific late step of large-subunit maturation downstream of rRNA refolding, clarifying biogenesis order.\",\n      \"evidence\": \"Cryo-EM of mtLSU assembly intermediates with genetic depletion of assembly factors and in vitro reconstitution in yeast\",\n      \"pmids\": [\"40865570\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"What triggers coordinate incorporation of bL35m with uL6m/uL16m/bL36m not defined\", \"Mammalian assembly order not directly addressed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Linking MRPL35 to ROS suppression in cancer cells established a pro-survival mitochondrial role beyond ribosome structure.\",\n      \"evidence\": \"siRNA knockdown in colorectal cancer cells with ROS, cell cycle, apoptosis, and membrane potential assays, plus NAC and overexpression rescue and xenograft\",\n      \"pmids\": [\"30862482\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular link between MRPL35 loss and ROS rise not mechanistically defined\", \"Relationship to its mitoribosomal assembly function unexplored\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Proteomic profiling after knockdown nominated downstream effectors of MRPL35 in proliferation and survival.\",\n      \"evidence\": \"shRNA knockdown with iTRAQ proteomics and Western validation in gastric carcinoma cells plus xenograft\",\n      \"pmids\": [\"33967557\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PICK1/BCL-XL/AGR2 changes are direct or secondary unknown\", \"No mechanistic connection to mitoribosome function\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Connecting MRPL35 to p53 suppression and cell cycle gene maintenance defined a transcriptional/signaling axis sustaining proliferation.\",\n      \"evidence\": \"Lentiviral shRNA knockdown in NSCLC cells with Western blot pathway readouts, colony formation, and xenograft imaging\",\n      \"pmids\": [\"38093266\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How a mitoribosomal protein represses p53 signaling not established\", \"Direct vs indirect regulation of cell cycle genes unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identifying a direct lncRNA partner raised the possibility of post-translational regulation of mitochondrial metabolic state via MRPL35.\",\n      \"evidence\": \"RNA-protein binding assay and metabolic profiling in macrophages in vitro and in vivo\",\n      \"pmids\": [\"37545364\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single binding interaction reported without detailed mechanistic follow-up on MRPL35's specific contribution\", \"Functional consequence of the lncRNA-MRPL35 interaction not isolated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defining USP39-mediated stabilization and the SLC7A5/glutamine link placed MRPL35 in a deubiquitination-controlled metabolic circuit in cancer.\",\n      \"evidence\": \"Cellular ubiquitination assay, knockdown/overexpression, glutamine metabolism assays, and epistasis rescue with SLC7A5 in NSCLC cells plus xenograft\",\n      \"pmids\": [\"38987867\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which MRPL35 regulates SLC7A5 expression unknown\", \"Whether stabilization affects mitoribosomal vs metabolic functions not separated\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Gain-of-function in a cholestasis model extended the ROS-suppressing role of MRPL35 to control of hepatic inflammatory signaling.\",\n      \"evidence\": \"Adenovirus-mediated MRPL35 overexpression in a rat PNAC model with pathway protein readouts and NAC mechanistic control\",\n      \"pmids\": [\"41049074\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the anti-inflammatory effect derives from mitoribosomal function unclear\", \"Upstream determinants of MRPL35 levels in this context undefined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the conserved mitoribosomal assembly-coupling function of MRPL35 mechanistically connects to its ROS-, p53-, and metabolism-modulating roles in mammalian cells remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No study bridges the yeast structural/assembly mechanism with the mammalian cancer signaling phenotypes\", \"Endogenous ligand of the PEBP domain unidentified\", \"Direct molecular targets in p53 and SLC7A5 regulation not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\"mitochondrial ribosome large subunit\", \"mitoribosomal central protuberance\"],\n    \"partners\": [\"Mrp7\", \"MrpL7\", \"MrpL36\", \"MrpL17\", \"MrpL28\", \"USP39\", \"ADPGK-AS1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":6,"faith_total":6,"faith_pct":100.0}}