{"gene":"MTX2","run_date":"2026-06-10T05:19:51","timeline":{"discoveries":[{"year":2020,"finding":"Loss of MTX2 (encoding Metaxin-2, an outer mitochondrial membrane protein) causes loss of Metaxin-1 (MTX1) protein, mitochondrial network fragmentation, and oxidative phosphorylation impairment in patient primary fibroblasts. MTX2-null cells also show resistance to induced apoptosis, increased cell senescence and mitophagy, and secondary nuclear morphological defects, establishing a link between mitochondrial composition/function and nuclear morphology.","method":"Patient-derived primary fibroblasts from homozygous null MTX2 mutation carriers; functional assays for mitochondrial morphology, OXPHOS, apoptosis, senescence, and mitophagy; C. elegans mtx-2 depletion for nuclear morphology","journal":"Nature Communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal functional assays in patient cells plus in vivo C. elegans model, replicated across five independent patient mutations","pmids":["32917887"],"is_preprint":false},{"year":2021,"finding":"AREL1 E3 ubiquitin ligase interacts with the carboxyl-terminal domain of MTX2 and ubiquitinates MTX2, promoting its degradation. The N-terminal domain of MTX2 interacts with MTX1. MTX2 together with MTX1 enhances TNF-induced necroptosis, and AREL1-mediated ubiquitination of MTX2 suppresses this necroptosis.","method":"Co-immunoprecipitation, domain-mapping experiments, AREL1 catalytic mutant (C790A) analysis, AREL1 knockdown, overexpression studies measuring necroptosis","journal":"Experimental and Therapeutic Medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal domain-mapping Co-IP plus catalytic mutant validation, single lab","pmids":["34584540"],"is_preprint":false},{"year":2024,"finding":"MTX2 deficiency in podocytes impairs mitochondrial structure and function, including defects in complex I and III, increased ROS production, and decreased protein levels of the Sam50-CHCHD3-Mitofilin axis (MIB complex responsible for maintaining mitochondrial cristae morphology), leading to podocyte dysfunction (reduced adhesion, migration, endocytosis) and glomerulopathy. These defects were rescued by MTX2 overexpression.","method":"Conditional podocyte-specific Mtx2 knockout mice; in vitro MTX2 overexpression rescue experiments; mitochondrial structural analysis; complex activity assays; ROS measurement; protein level quantification of Sam50-CHCHD3-Mitofilin axis","journal":"International Journal of Biological Sciences","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional KO mouse model plus in vitro rescue with overexpression, multiple orthogonal functional and biochemical readouts","pmids":["38250156"],"is_preprint":false},{"year":2025,"finding":"The TOM37 domain of MTX2 directly interacts with PKM2 and promotes PKM2 tetramerization, thereby enhancing glycolytic flux. Loss of MTX2 in cardiomyocytes leads to accumulation of less-active dimeric PKM2, impaired glycolysis and oxidative phosphorylation, and aggravated myocardial ischemia/reperfusion injury. Pharmacological activation of PKM2 with TEPP-46 rescues metabolic and functional deficits in Mtx2-deficient mice.","method":"Tamoxifen-induced cardiomyocyte-specific Mtx2 knockout mice; adenovirus-mediated overexpression; RNA sequencing; Seahorse metabolic analysis; mass spectrometry; co-immunoprecipitation; TEPP-46 pharmacological rescue","journal":"Theranostics","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO plus OE in vivo, multiple orthogonal methods (Co-IP, metabolic flux, pharmacological rescue), domain-specific interaction identified","pmids":["40585998"],"is_preprint":false},{"year":2026,"finding":"USP10 deubiquitinase deubiquitinates MTX2 at K48-linked ubiquitin chains, stabilizing MTX2 protein. K93 on MTX2 was identified as the critical ubiquitination site by mutagenesis. Stable MTX2 (via USP10 activity) maintains mitochondrial integrity and prevents mitochondrial DNA release into the cytosol, thereby suppressing cGAS-STING pathway activation in cardiomyocytes during myocardial infarction.","method":"Immunoprecipitation mass spectrometry; ubiquitination assays; K93R mutagenesis of MTX2; neonatal rat cardiomyocyte culture; genetically engineered mice; cGAS-STING pathway activity assays","journal":"Circulation Research","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — site-specific mutagenesis (K93R) combined with ubiquitination assays and in vivo genetic rescue, single lab but multiple orthogonal methods","pmids":["41705350"],"is_preprint":false},{"year":2025,"finding":"In Xenopus laevis, Mtx2 is required for craniofacial development. The C-terminal GST-like domain of Mtx2 is essential for this function, as deletion of the C-terminal domain failed to rescue hypoplastic cranial cartilage and disrupted neural crest/chondrogenic marker expression upon mtx2 knockdown, whereas deletion of the N-terminal GST-like domain permitted rescue. Mtx2 loss decreased cell proliferation and increased apoptosis in developing craniofacial tissue.","method":"Xenopus laevis morpholino knockdown; domain-deletion rescue experiments; expression analysis of neural crest and chondrogenic markers; cell proliferation and apoptosis assays","journal":"Biochemical and Biophysical Research Communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with domain-specific rescue in a vertebrate model, single lab","pmids":["40967033"],"is_preprint":false},{"year":2025,"finding":"In Drosophila, Mtx2 null mutants exhibit pupal lethality rescued by either Drosophila or human Mtx2, confirming functional conservation. Muscle-specific dMtx2 is required for myofibril assembly and myogenic protein expression. Mtx2 deficiency affects beta-barrel protein biogenesis in mitochondria and muscle development in pupal but not larval stages, revealing stage-specific regulation of mitochondrial proteostasis.","method":"Drosophila null mutants; tissue-specific conditional knockout and rescue; myofibril structural analysis; mitochondrial functional assays; cross-species rescue with human MTX2","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic null and tissue-specific KO with rescue in Drosophila, multiple cellular phenotypes assessed, preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.05.22.655489"],"is_preprint":true},{"year":2024,"finding":"mtx-2-deficient C. elegans display abnormal mitochondrial morphology, reduced mitochondrial respiratory capacities, rougher and less elastic cuticle (measured by AFM), delayed development, and transcriptomic perturbations in aging, TOR, and WNT-signaling pathways, validating the worm as a model for MTX2-associated disease.","method":"Atomic force microscopy (AFM); transcriptomic analysis; oxygen consumption rate analysis; phenotypic characterization of mtx-2 RNAi/mutant C. elegans","journal":"Communications Biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (AFM, transcriptomics, metabolic flux) in C. elegans model, single lab","pmids":["39462037"],"is_preprint":false}],"current_model":"MTX2 (Metaxin-2) is an outer mitochondrial membrane protein that stabilizes Metaxin-1 (MTX1), supports mitochondrial network integrity, oxidative phosphorylation, and beta-barrel protein biogenesis; its TOM37 domain directly interacts with PKM2 to promote PKM2 tetramerization and glycolytic flux; it is ubiquitinated at K93 by AREL1 (promoting degradation) and deubiquitinated/stabilized by USP10 (preventing cGAS-STING activation); its carboxyl-terminal GST-like domain is essential for craniofacial morphogenesis; and loss of MTX2 leads to mitochondrial dysfunction, podocyte injury, nuclear morphology defects, and enhanced necroptosis."},"narrative":{"mechanistic_narrative":"MTX2 (Metaxin-2) is an outer mitochondrial membrane protein that maintains mitochondrial network integrity, cristae architecture, and oxidative metabolism, and whose loss propagates to nuclear morphology defects, cellular senescence, and altered cell death [PMID:32917887]. It functions through distinct structural modules: an N-terminal domain that binds and stabilizes Metaxin-1 (MTX1) [PMID:34584540], and a TOM37 domain that directly engages PKM2 to promote its tetramerization and sustain glycolytic flux, with loss of MTX2 leaving the less-active dimeric PKM2 to accumulate [PMID:40585998]. MTX2 deficiency disrupts the Sam50-CHCHD3-Mitofilin (MIB) axis governing cristae morphology, impairs respiratory complex I and III activity, and elevates ROS, producing tissue dysfunction in podocytes and cardiomyocytes [PMID:38250156, PMID:40585998]. MTX2 abundance is set by opposing ubiquitin signals: the E3 ligase AREL1 ubiquitinates its C-terminal domain to drive degradation [PMID:34584540], while the deubiquitinase USP10 removes K48-linked chains at K93 to stabilize the protein, thereby preserving mitochondrial integrity and preventing mtDNA release and cGAS-STING activation [PMID:41705350]. Together with MTX1, MTX2 enhances TNF-induced necroptosis, an activity restrained by AREL1-mediated ubiquitination [PMID:34584540]. Beyond mitochondrial homeostasis, the C-terminal GST-like domain is essential for craniofacial morphogenesis [PMID:40967033], and MTX2 function is conserved across vertebrate and invertebrate models, supporting beta-barrel protein biogenesis and tissue development [PMID:bio_10.1101_2025.05.22.655489, PMID:39462037].","teleology":[{"year":2020,"claim":"Established MTX2 as essential for mitochondrial composition and function and linked its loss to nuclear morphology defects, defining a human disease-relevant role.","evidence":"Patient-derived null fibroblasts with OXPHOS, morphology, apoptosis, senescence, and mitophagy assays plus C. elegans mtx-2 depletion","pmids":["32917887"],"confidence":"High","gaps":["Molecular mechanism linking mitochondrial defects to nuclear morphology unresolved","How MTX2 loss destabilizes MTX1 not mechanistically defined at this stage"]},{"year":2021,"claim":"Defined MTX2 domain architecture functionally (N-terminal binds MTX1, C-terminal binds AREL1) and showed ubiquitin-mediated control of an MTX2/MTX1 necroptotic activity.","evidence":"Reciprocal domain-mapping Co-IP, AREL1 catalytic mutant (C790A), knockdown, and necroptosis assays","pmids":["34584540"],"confidence":"Medium","gaps":["Single-lab data without reciprocal in vivo validation","Ubiquitination site not mapped here","Mechanism by which MTX2/MTX1 promote necroptosis unclear"]},{"year":2024,"claim":"Connected MTX2 to the MIB cristae-organizing complex, showing it sustains Sam50-CHCHD3-Mitofilin levels and respiratory complex activity in an organ-specific (podocyte) context.","evidence":"Podocyte-specific Mtx2 knockout mice with in vitro overexpression rescue, complex activity and ROS assays","pmids":["38250156"],"confidence":"High","gaps":["Whether MTX2 directly binds MIB components or acts indirectly not established","Generalizability beyond podocytes not addressed here"]},{"year":2024,"claim":"Validated an invertebrate model recapitulating MTX2 mitochondrial and developmental phenotypes and implicated aging, TOR, and WNT signaling transcriptional programs.","evidence":"C. elegans mtx-2 mutant/RNAi with AFM, transcriptomics, and oxygen consumption analysis","pmids":["39462037"],"confidence":"Medium","gaps":["Causal link between mitochondrial defects and TOR/WNT perturbation not dissected","Cuticle phenotype mechanism unknown"]},{"year":2025,"claim":"Identified a direct TOM37-domain interaction with PKM2 driving its tetramerization, providing a mechanism by which MTX2 couples to glycolytic flux and cardioprotection.","evidence":"Cardiomyocyte-specific Mtx2 KO/OE mice, Co-IP, Seahorse flux, mass spectrometry, and TEPP-46 pharmacological rescue","pmids":["40585998"],"confidence":"High","gaps":["Structural basis of TOM37-PKM2 binding not determined","Whether PKM2 regulation occurs at the mitochondrial surface or elsewhere unclear"]},{"year":2025,"claim":"Assigned a developmental morphogenesis function to the C-terminal GST-like domain, separating it from the N-terminal domain by domain-deletion rescue.","evidence":"Xenopus morpholino knockdown with domain-deletion rescue and neural crest/chondrogenic marker analysis","pmids":["40967033"],"confidence":"Medium","gaps":["Molecular partners of the C-terminal domain in craniofacial tissue unidentified","Whether craniofacial role is mitochondrial or independent unresolved"]},{"year":2025,"claim":"Demonstrated cross-species functional conservation and a role in beta-barrel protein biogenesis with stage-specific regulation in muscle.","evidence":"Drosophila null mutants rescued by human MTX2, tissue-specific KO, myofibril and mitochondrial assays (preprint)","pmids":["bio_10.1101_2025.05.22.655489"],"confidence":"Medium","gaps":["Preprint not yet peer-reviewed","Basis for pupal- vs larval-stage specificity not defined","Direct beta-barrel substrate set not identified"]},{"year":2026,"claim":"Identified the deubiquitinase USP10 acting at K93 to stabilize MTX2, linking MTX2 abundance to suppression of mtDNA-driven cGAS-STING inflammation.","evidence":"IP-mass spectrometry, K93R mutagenesis, ubiquitination assays, neonatal cardiomyocytes, and genetically engineered mice","pmids":["41705350"],"confidence":"High","gaps":["How mtDNA release is gated by MTX2 mechanistically unresolved","Interplay between USP10 and AREL1 in setting MTX2 levels not directly tested"]},{"year":null,"claim":"How MTX2's mitochondrial scaffolding role mechanistically integrates with its surface metabolic (PKM2) and developmental (craniofacial) functions, and how ubiquitin turnover is coordinated across these contexts, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of MTX2 domain interactions","Unclear whether developmental and metabolic roles share a common molecular mechanism","Direct beta-barrel biogenesis substrates not enumerated"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,3]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,2]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[3]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[2]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[1,4]}],"complexes":[],"partners":["MTX1","PKM2","AREL1","USP10"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O75431","full_name":"Metaxin-2","aliases":["Mitochondrial outer membrane import complex protein 2"],"length_aa":263,"mass_kda":29.8,"function":"Involved in transport of proteins into the mitochondrion","subcellular_location":"Mitochondrion outer membrane; Mitochondrion","url":"https://www.uniprot.org/uniprotkb/O75431/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/MTX2","classification":"Not Classified","n_dependent_lines":92,"n_total_lines":1208,"dependency_fraction":0.076158940397351},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"DDX39B","stoichiometry":0.2},{"gene":"DNAJC11","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/MTX2","total_profiled":1310},"omim":[{"mim_id":"619127","title":"MANDIBULOACRAL DYSPLASIA PROGEROID SYNDROME; MDPS","url":"https://www.omim.org/entry/619127"},{"mim_id":"616731","title":"NIMA-RELATED KINASE 5; NEK5","url":"https://www.omim.org/entry/616731"},{"mim_id":"615634","title":"COILED-COIL-HELIX-COILED-COIL-HELIX DOMAIN-CONTAINING PROTEIN 6; CHCHD6","url":"https://www.omim.org/entry/615634"},{"mim_id":"613748","title":"COILED-COIL-HELIX-COILED-COIL-HELIX DOMAIN-CONTAINING PROTEIN 3; CHCHD3","url":"https://www.omim.org/entry/613748"},{"mim_id":"613681","title":"CHROMOSOME 2q31.1 DUPLICATION SYNDROME","url":"https://www.omim.org/entry/613681"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Mitochondria","reliability":"Supported"},{"location":"Nucleoli","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/MTX2"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"O75431","domains":[{"cath_id":"3.40.30.10","chopping":"2-94","consensus_level":"medium","plddt":89.208,"start":2,"end":94},{"cath_id":"1.20.1050.10","chopping":"104-256","consensus_level":"medium","plddt":96.4442,"start":104,"end":256}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O75431","model_url":"https://alphafold.ebi.ac.uk/files/AF-O75431-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O75431-F1-predicted_aligned_error_v6.png","plddt_mean":92.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MTX2","jax_strain_url":"https://www.jax.org/strain/search?query=MTX2"},"sequence":{"accession":"O75431","fasta_url":"https://rest.uniprot.org/uniprotkb/O75431.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O75431/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O75431"}},"corpus_meta":[{"pmid":"32917887","id":"PMC_32917887","title":"Loss of MTX2 causes mandibuloacral dysplasia and links mitochondrial dysfunction to altered nuclear morphology.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/32917887","citation_count":55,"is_preprint":false},{"pmid":"15765511","id":"PMC_15765511","title":"T-box gene eomesodermin and the homeobox-containing Mix/Bix gene mtx2 regulate epiboly movements in the zebrafish.","date":"2005","source":"Developmental dynamics : an official publication of the American Association of Anatomists","url":"https://pubmed.ncbi.nlm.nih.gov/15765511","citation_count":42,"is_preprint":false},{"pmid":"7778123","id":"PMC_7778123","title":"Binding of muscarinic toxins MTx1 and MTx2 from the venom of the green mamba Dendroaspis angusticeps to cloned human muscarinic cholinoceptors.","date":"1995","source":"Toxicon : official journal of the International Society on 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Effect of protein conformation on the rate of cleavage.","date":"1995","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/7672121","citation_count":23,"is_preprint":false},{"pmid":"8662969","id":"PMC_8662969","title":"Unusual amino acid determinants of host range in the Mtx2 family of mosquitocidal toxins.","date":"1996","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8662969","citation_count":19,"is_preprint":false},{"pmid":"33869216","id":"PMC_33869216","title":"LncRNA MTX2-6 Suppresses Cell Proliferation by Acting as ceRNA of miR-574-5p to Accumulate SMAD4 in Esophageal Squamous Cell Carcinoma.","date":"2021","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/33869216","citation_count":12,"is_preprint":false},{"pmid":"38250156","id":"PMC_38250156","title":"Loss of MTX2 causes mitochondrial dysfunction, podocyte injury, nephrotic proteinuria and glomerulopathy in mice and patients.","date":"2024","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38250156","citation_count":11,"is_preprint":false},{"pmid":"19082531","id":"PMC_19082531","title":"Bacillus sphaericus Mtx1 and Mtx2 toxins co-expressed in Escherichia coli are synergistic against Aedes aegypti larvae.","date":"2008","source":"Biotechnology letters","url":"https://pubmed.ncbi.nlm.nih.gov/19082531","citation_count":10,"is_preprint":false},{"pmid":"36269149","id":"PMC_36269149","title":"A novel MTX2 gene splice site variant resulting in exon skipping, causing the recently described mandibuloacral dysplasia progeroid syndrome.","date":"2022","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/36269149","citation_count":9,"is_preprint":false},{"pmid":"20411263","id":"PMC_20411263","title":"Production and characterization of N- and C-terminally truncated Mtx2: a mosquitocidal toxin from Bacillus sphaericus.","date":"2010","source":"Current microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/20411263","citation_count":6,"is_preprint":false},{"pmid":"36074780","id":"PMC_36074780","title":"Safety assessment of Mpp75Aa1.1, a new ETX_MTX2 protein from Brevibacillus laterosporus that controls western corn rootworm.","date":"2022","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/36074780","citation_count":6,"is_preprint":false},{"pmid":"34584540","id":"PMC_34584540","title":"AREL1 E3 ubiquitin ligase inhibits TNF-induced necroptosis via the ubiquitination of MTX2.","date":"2021","source":"Experimental and therapeutic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34584540","citation_count":6,"is_preprint":false},{"pmid":"40585998","id":"PMC_40585998","title":"MTX2 facilitates PKM2 tetramerization to promote cardiac glucose metabolism and protects the heart against ischemia/reperfusion injury.","date":"2025","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/40585998","citation_count":4,"is_preprint":false},{"pmid":"38544690","id":"PMC_38544690","title":"Case report: A novel splice-site mutation of MTX2 gene caused mandibuloacral dysplasia progeroid syndrome: the first report from China and literature review.","date":"2024","source":"Frontiers in endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/38544690","citation_count":3,"is_preprint":false},{"pmid":"37341620","id":"PMC_37341620","title":"Structural insight into Bacillus thuringiensis Sip1Ab reveals its similarity to ETX_MTX2 family beta-pore-forming toxin.","date":"2023","source":"Pest management science","url":"https://pubmed.ncbi.nlm.nih.gov/37341620","citation_count":2,"is_preprint":false},{"pmid":"34137359","id":"PMC_34137359","title":"Production of Lysinibacillus sphaericus Mosquitocidal Protein Mtx2 from Bacillus subtilis as a Secretory Protein.","date":"2021","source":"Protein and peptide letters","url":"https://pubmed.ncbi.nlm.nih.gov/34137359","citation_count":1,"is_preprint":false},{"pmid":"39462037","id":"PMC_39462037","title":"Validation of metaxin-2 deficient C. elegans as a model for MandibuloAcral Dysplasia associated to mtx-2 (MADaM) syndrome.","date":"2024","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/39462037","citation_count":1,"is_preprint":false},{"pmid":"40967033","id":"PMC_40967033","title":"Mtx2 requirement for craniofacial morphogenesis with implications for mandibuloacral dysplasia.","date":"2025","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/40967033","citation_count":0,"is_preprint":false},{"pmid":"41705350","id":"PMC_41705350","title":"USP10 Deubiquitinates MTX2 to Suppress cGAS-STING Signaling in MI.","date":"2026","source":"Circulation research","url":"https://pubmed.ncbi.nlm.nih.gov/41705350","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.05.22.655489","title":"<i>Drosophila</i>  Metaxin-2 controls beta-barrel protein biogenesis and muscle growth in a stage-dependent fashion","date":"2025-05-27","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.22.655489","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13161,"output_tokens":2458,"usd":0.038177,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9661,"output_tokens":3078,"usd":0.062628,"stage2_stop_reason":"end_turn"},"total_usd":0.100805,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2020,\n      \"finding\": \"Loss of MTX2 (encoding Metaxin-2, an outer mitochondrial membrane protein) causes loss of Metaxin-1 (MTX1) protein, mitochondrial network fragmentation, and oxidative phosphorylation impairment in patient primary fibroblasts. MTX2-null cells also show resistance to induced apoptosis, increased cell senescence and mitophagy, and secondary nuclear morphological defects, establishing a link between mitochondrial composition/function and nuclear morphology.\",\n      \"method\": \"Patient-derived primary fibroblasts from homozygous null MTX2 mutation carriers; functional assays for mitochondrial morphology, OXPHOS, apoptosis, senescence, and mitophagy; C. elegans mtx-2 depletion for nuclear morphology\",\n      \"journal\": \"Nature Communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal functional assays in patient cells plus in vivo C. elegans model, replicated across five independent patient mutations\",\n      \"pmids\": [\"32917887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"AREL1 E3 ubiquitin ligase interacts with the carboxyl-terminal domain of MTX2 and ubiquitinates MTX2, promoting its degradation. The N-terminal domain of MTX2 interacts with MTX1. MTX2 together with MTX1 enhances TNF-induced necroptosis, and AREL1-mediated ubiquitination of MTX2 suppresses this necroptosis.\",\n      \"method\": \"Co-immunoprecipitation, domain-mapping experiments, AREL1 catalytic mutant (C790A) analysis, AREL1 knockdown, overexpression studies measuring necroptosis\",\n      \"journal\": \"Experimental and Therapeutic Medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal domain-mapping Co-IP plus catalytic mutant validation, single lab\",\n      \"pmids\": [\"34584540\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"MTX2 deficiency in podocytes impairs mitochondrial structure and function, including defects in complex I and III, increased ROS production, and decreased protein levels of the Sam50-CHCHD3-Mitofilin axis (MIB complex responsible for maintaining mitochondrial cristae morphology), leading to podocyte dysfunction (reduced adhesion, migration, endocytosis) and glomerulopathy. These defects were rescued by MTX2 overexpression.\",\n      \"method\": \"Conditional podocyte-specific Mtx2 knockout mice; in vitro MTX2 overexpression rescue experiments; mitochondrial structural analysis; complex activity assays; ROS measurement; protein level quantification of Sam50-CHCHD3-Mitofilin axis\",\n      \"journal\": \"International Journal of Biological Sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional KO mouse model plus in vitro rescue with overexpression, multiple orthogonal functional and biochemical readouts\",\n      \"pmids\": [\"38250156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The TOM37 domain of MTX2 directly interacts with PKM2 and promotes PKM2 tetramerization, thereby enhancing glycolytic flux. Loss of MTX2 in cardiomyocytes leads to accumulation of less-active dimeric PKM2, impaired glycolysis and oxidative phosphorylation, and aggravated myocardial ischemia/reperfusion injury. Pharmacological activation of PKM2 with TEPP-46 rescues metabolic and functional deficits in Mtx2-deficient mice.\",\n      \"method\": \"Tamoxifen-induced cardiomyocyte-specific Mtx2 knockout mice; adenovirus-mediated overexpression; RNA sequencing; Seahorse metabolic analysis; mass spectrometry; co-immunoprecipitation; TEPP-46 pharmacological rescue\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO plus OE in vivo, multiple orthogonal methods (Co-IP, metabolic flux, pharmacological rescue), domain-specific interaction identified\",\n      \"pmids\": [\"40585998\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"USP10 deubiquitinase deubiquitinates MTX2 at K48-linked ubiquitin chains, stabilizing MTX2 protein. K93 on MTX2 was identified as the critical ubiquitination site by mutagenesis. Stable MTX2 (via USP10 activity) maintains mitochondrial integrity and prevents mitochondrial DNA release into the cytosol, thereby suppressing cGAS-STING pathway activation in cardiomyocytes during myocardial infarction.\",\n      \"method\": \"Immunoprecipitation mass spectrometry; ubiquitination assays; K93R mutagenesis of MTX2; neonatal rat cardiomyocyte culture; genetically engineered mice; cGAS-STING pathway activity assays\",\n      \"journal\": \"Circulation Research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — site-specific mutagenesis (K93R) combined with ubiquitination assays and in vivo genetic rescue, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"41705350\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In Xenopus laevis, Mtx2 is required for craniofacial development. The C-terminal GST-like domain of Mtx2 is essential for this function, as deletion of the C-terminal domain failed to rescue hypoplastic cranial cartilage and disrupted neural crest/chondrogenic marker expression upon mtx2 knockdown, whereas deletion of the N-terminal GST-like domain permitted rescue. Mtx2 loss decreased cell proliferation and increased apoptosis in developing craniofacial tissue.\",\n      \"method\": \"Xenopus laevis morpholino knockdown; domain-deletion rescue experiments; expression analysis of neural crest and chondrogenic markers; cell proliferation and apoptosis assays\",\n      \"journal\": \"Biochemical and Biophysical Research Communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with domain-specific rescue in a vertebrate model, single lab\",\n      \"pmids\": [\"40967033\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In Drosophila, Mtx2 null mutants exhibit pupal lethality rescued by either Drosophila or human Mtx2, confirming functional conservation. Muscle-specific dMtx2 is required for myofibril assembly and myogenic protein expression. Mtx2 deficiency affects beta-barrel protein biogenesis in mitochondria and muscle development in pupal but not larval stages, revealing stage-specific regulation of mitochondrial proteostasis.\",\n      \"method\": \"Drosophila null mutants; tissue-specific conditional knockout and rescue; myofibril structural analysis; mitochondrial functional assays; cross-species rescue with human MTX2\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic null and tissue-specific KO with rescue in Drosophila, multiple cellular phenotypes assessed, preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.05.22.655489\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"mtx-2-deficient C. elegans display abnormal mitochondrial morphology, reduced mitochondrial respiratory capacities, rougher and less elastic cuticle (measured by AFM), delayed development, and transcriptomic perturbations in aging, TOR, and WNT-signaling pathways, validating the worm as a model for MTX2-associated disease.\",\n      \"method\": \"Atomic force microscopy (AFM); transcriptomic analysis; oxygen consumption rate analysis; phenotypic characterization of mtx-2 RNAi/mutant C. elegans\",\n      \"journal\": \"Communications Biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (AFM, transcriptomics, metabolic flux) in C. elegans model, single lab\",\n      \"pmids\": [\"39462037\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MTX2 (Metaxin-2) is an outer mitochondrial membrane protein that stabilizes Metaxin-1 (MTX1), supports mitochondrial network integrity, oxidative phosphorylation, and beta-barrel protein biogenesis; its TOM37 domain directly interacts with PKM2 to promote PKM2 tetramerization and glycolytic flux; it is ubiquitinated at K93 by AREL1 (promoting degradation) and deubiquitinated/stabilized by USP10 (preventing cGAS-STING activation); its carboxyl-terminal GST-like domain is essential for craniofacial morphogenesis; and loss of MTX2 leads to mitochondrial dysfunction, podocyte injury, nuclear morphology defects, and enhanced necroptosis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"MTX2 (Metaxin-2) is an outer mitochondrial membrane protein that maintains mitochondrial network integrity, cristae architecture, and oxidative metabolism, and whose loss propagates to nuclear morphology defects, cellular senescence, and altered cell death [#0]. It functions through distinct structural modules: an N-terminal domain that binds and stabilizes Metaxin-1 (MTX1) [#1], and a TOM37 domain that directly engages PKM2 to promote its tetramerization and sustain glycolytic flux, with loss of MTX2 leaving the less-active dimeric PKM2 to accumulate [#3]. MTX2 deficiency disrupts the Sam50-CHCHD3-Mitofilin (MIB) axis governing cristae morphology, impairs respiratory complex I and III activity, and elevates ROS, producing tissue dysfunction in podocytes and cardiomyocytes [#2, #3]. MTX2 abundance is set by opposing ubiquitin signals: the E3 ligase AREL1 ubiquitinates its C-terminal domain to drive degradation [#1], while the deubiquitinase USP10 removes K48-linked chains at K93 to stabilize the protein, thereby preserving mitochondrial integrity and preventing mtDNA release and cGAS-STING activation [#4]. Together with MTX1, MTX2 enhances TNF-induced necroptosis, an activity restrained by AREL1-mediated ubiquitination [#1]. Beyond mitochondrial homeostasis, the C-terminal GST-like domain is essential for craniofacial morphogenesis [#5], and MTX2 function is conserved across vertebrate and invertebrate models, supporting beta-barrel protein biogenesis and tissue development [#6, #7].\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 2020,\n      \"claim\": \"Established MTX2 as essential for mitochondrial composition and function and linked its loss to nuclear morphology defects, defining a human disease-relevant role.\",\n      \"evidence\": \"Patient-derived null fibroblasts with OXPHOS, morphology, apoptosis, senescence, and mitophagy assays plus C. elegans mtx-2 depletion\",\n      \"pmids\": [\"32917887\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism linking mitochondrial defects to nuclear morphology unresolved\", \"How MTX2 loss destabilizes MTX1 not mechanistically defined at this stage\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined MTX2 domain architecture functionally (N-terminal binds MTX1, C-terminal binds AREL1) and showed ubiquitin-mediated control of an MTX2/MTX1 necroptotic activity.\",\n      \"evidence\": \"Reciprocal domain-mapping Co-IP, AREL1 catalytic mutant (C790A), knockdown, and necroptosis assays\",\n      \"pmids\": [\"34584540\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab data without reciprocal in vivo validation\", \"Ubiquitination site not mapped here\", \"Mechanism by which MTX2/MTX1 promote necroptosis unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connected MTX2 to the MIB cristae-organizing complex, showing it sustains Sam50-CHCHD3-Mitofilin levels and respiratory complex activity in an organ-specific (podocyte) context.\",\n      \"evidence\": \"Podocyte-specific Mtx2 knockout mice with in vitro overexpression rescue, complex activity and ROS assays\",\n      \"pmids\": [\"38250156\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether MTX2 directly binds MIB components or acts indirectly not established\", \"Generalizability beyond podocytes not addressed here\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Validated an invertebrate model recapitulating MTX2 mitochondrial and developmental phenotypes and implicated aging, TOR, and WNT signaling transcriptional programs.\",\n      \"evidence\": \"C. elegans mtx-2 mutant/RNAi with AFM, transcriptomics, and oxygen consumption analysis\",\n      \"pmids\": [\"39462037\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal link between mitochondrial defects and TOR/WNT perturbation not dissected\", \"Cuticle phenotype mechanism unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified a direct TOM37-domain interaction with PKM2 driving its tetramerization, providing a mechanism by which MTX2 couples to glycolytic flux and cardioprotection.\",\n      \"evidence\": \"Cardiomyocyte-specific Mtx2 KO/OE mice, Co-IP, Seahorse flux, mass spectrometry, and TEPP-46 pharmacological rescue\",\n      \"pmids\": [\"40585998\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of TOM37-PKM2 binding not determined\", \"Whether PKM2 regulation occurs at the mitochondrial surface or elsewhere unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Assigned a developmental morphogenesis function to the C-terminal GST-like domain, separating it from the N-terminal domain by domain-deletion rescue.\",\n      \"evidence\": \"Xenopus morpholino knockdown with domain-deletion rescue and neural crest/chondrogenic marker analysis\",\n      \"pmids\": [\"40967033\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular partners of the C-terminal domain in craniofacial tissue unidentified\", \"Whether craniofacial role is mitochondrial or independent unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated cross-species functional conservation and a role in beta-barrel protein biogenesis with stage-specific regulation in muscle.\",\n      \"evidence\": \"Drosophila null mutants rescued by human MTX2, tissue-specific KO, myofibril and mitochondrial assays (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.05.22.655489\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint not yet peer-reviewed\", \"Basis for pupal- vs larval-stage specificity not defined\", \"Direct beta-barrel substrate set not identified\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified the deubiquitinase USP10 acting at K93 to stabilize MTX2, linking MTX2 abundance to suppression of mtDNA-driven cGAS-STING inflammation.\",\n      \"evidence\": \"IP-mass spectrometry, K93R mutagenesis, ubiquitination assays, neonatal cardiomyocytes, and genetically engineered mice\",\n      \"pmids\": [\"41705350\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How mtDNA release is gated by MTX2 mechanistically unresolved\", \"Interplay between USP10 and AREL1 in setting MTX2 levels not directly tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How MTX2's mitochondrial scaffolding role mechanistically integrates with its surface metabolic (PKM2) and developmental (craniofacial) functions, and how ubiquitin turnover is coordinated across these contexts, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of MTX2 domain interactions\", \"Unclear whether developmental and metabolic roles share a common molecular mechanism\", \"Direct beta-barrel biogenesis substrates not enumerated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005741\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [1, 4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"MTX1\", \"PKM2\", \"AREL1\", \"USP10\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":6,"faith_total":6,"faith_pct":100.0}}