{"gene":"SUCLG1","run_date":"2026-04-28T21:42:57","timeline":{"discoveries":[{"year":2010,"finding":"SUCLG1 encodes the alpha subunit of succinate-CoA ligase (SUCL), a heterodimeric mitochondrial enzyme; when SUCLG1 protein is absent, SUCLA2 protein is also absent in fibroblasts, indicating that SUCLG1 (alpha subunit) is required to stabilize the SUCLA2 (beta subunit) heterodimer partner, preventing its degradation.","method":"Western blot analysis of patient fibroblasts lacking SUCLG1 protein; minigene expression system to confirm splicing mutation","journal":"Journal of medical genetics","confidence":"High","confidence_rationale":"Tier 2 — reciprocal western blot in patient cells, replicated across multiple subsequent studies","pmids":["20693550"],"is_preprint":false},{"year":2018,"finding":"Mutated SUCLG1 (p.Ala209Glu) causes loss of SUCLG1 protein, severely reduced SUCLA2 and SUCLG2 protein levels, impaired mitochondrial substrate-level phosphorylation (mSLP), mislocalization of SUCLG2 away from the mitochondrial network, and increased mitochondrial fragmentation, without changes in ETC activities or mtDNA levels.","method":"Enzyme activity assay for mSLP, immunoblot analysis, confocal triple immunocytochemistry, oxygen consumption and extracellular acidification rate measurements in skin fibroblasts","journal":"Molecular genetics and metabolism","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (enzyme assay, imaging, respirometry) in patient-derived cells, single lab","pmids":["30470562"],"is_preprint":false},{"year":2016,"finding":"Loss of SUCLG1 protein leads to loss of SCS enzyme activity, mtDNA depletion, and cellular respiration defects; ectopic expression of wild-type SUCLG1 in patient fibroblasts rescues all these phenotypes, confirming SUCLG1 is required for SCS activity, mtDNA maintenance, and mitochondrial respiration.","method":"SCS enzyme activity assay, mtDNA quantification, cellular respiration assay, rescue by ectopic wild-type SUCLG1 expression in patient fibroblasts","journal":"Molecular genetics and metabolism","confidence":"High","confidence_rationale":"Tier 2 — rescue experiment with multiple functional readouts, single lab","pmids":["27484306"],"is_preprint":false},{"year":2024,"finding":"SUCLG1 restricts succinyl-CoA levels to suppress succinylation of mitochondrial RNA polymerase (POLRMT) at lysine 622; this hyposuccinylation maintains POLRMT interaction with mtDNA and mitochondrial transcription factors, preserving mtDNA transcription and mitochondrial biogenesis. FLT3 mutations upregulate SUCLG1 expression to reduce succinyl-CoA and POLRMT succinylation, enhancing mitobiogenesis and leukemia progression.","method":"Succinylation proteomics, site-directed mutagenesis (K622 succinylation site), Co-IP of POLRMT with mtDNA/transcription factors, genetic depletion of SUCLG1 and POLRMT in mouse and humanized leukemia models, succinyl-CoA level measurement in clinical samples","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods including mutagenesis, Co-IP, in vivo models, and clinical validation","pmids":["38649537"],"is_preprint":false},{"year":2009,"finding":"SUCLG1 encodes the alpha subunit of succinate-CoA ligase; missense mutations in SUCLG1 cause the encephalomyopathic mtDNA depletion syndrome with methylmalonic aciduria, phenotypically similar to SUCLA2 mutations.","method":"Genetic sequencing, clinical biochemical profiling (methylmalonic aciduria, lactic acidosis), mtDNA quantification","journal":"European journal of pediatrics","confidence":"Medium","confidence_rationale":"Tier 3 — genetic and biochemical characterization, single case report","pmids":["19526370"],"is_preprint":false},{"year":2017,"finding":"The p.M14T mutation in SUCLG1 is located in the mitochondrial targeting sequence; in-silico analysis predicted this mutation alters protein stability and mitochondrial translocation, and patients showed decreased mtDNA copy number.","method":"Mutational analysis, in-silico structural prediction, real-time PCR for mtDNA quantification","journal":"Biochemical and biophysical research communications","confidence":"Low","confidence_rationale":"Tier 4 — primarily computational prediction with indirect functional evidence (mtDNA depletion)","pmids":["29217198"],"is_preprint":false},{"year":2026,"finding":"SUCLG1 is butyrylated at K90 in the context of HFpEF, which impairs its enzymatic function in the TCA cycle, reducing succinate and ATP production; SIRT4 acts as a debutyrylase for SUCLG1, and reduced SIRT4 expression leads to SUCLG1 hyperbutyrylation and impaired enzymatic activity.","method":"Butyrylome proteomic screening, SIRT4 inhibitor and overexpression experiments, in vivo mouse HFpEF model, cellular model with phenylephrine","journal":"Pharmacological research","confidence":"Medium","confidence_rationale":"Tier 2 — proteomic identification + genetic manipulation (overexpression/inhibitor) with functional enzymatic readout, single lab","pmids":["41991142"],"is_preprint":false},{"year":2025,"finding":"SUCLG1 promotes mitochondrial fusion and enhances aerobic respiration (without affecting glycolysis) in plexiform neurofibroma cells; SUCLG1 knockdown reduces proliferation and migration, while overexpression enhances these processes and upregulates SLC25A1 expression.","method":"SUCLG1 knockdown and overexpression, Seahorse assay for aerobic respiration and glycolysis, electron microscopy of mitochondria, flow cytometry, qPCR and western blot","journal":"International journal of oncology","confidence":"Medium","confidence_rationale":"Tier 2 — loss- and gain-of-function with multiple orthogonal functional readouts, single lab","pmids":["39749698"],"is_preprint":false}],"current_model":"SUCLG1 encodes the alpha subunit of mitochondrial succinate-CoA ligase (SUCL), which is essential for TCA cycle substrate-level phosphorylation, mtDNA maintenance, and stabilization of the beta subunits SUCLA2 and SUCLG2; additionally, SUCLG1 controls succinyl-CoA levels to suppress succinylation of mitochondrial RNA polymerase (POLRMT) at K622, thereby maintaining mtDNA transcription and mitochondrial biogenesis, while its enzymatic activity is itself regulated by post-translational modifications including butyrylation at K90 (removed by SIRT4)."},"narrative":{"teleology":[{"year":2009,"claim":"Establishing that SUCLG1 is a disease gene: before this, the genetic basis of some encephalomyopathic mtDNA depletion cases was unknown; identification of biallelic SUCLG1 mutations linked the alpha subunit to a Mendelian mtDNA depletion syndrome with methylmalonic aciduria, paralleling SUCLA2-associated disease.","evidence":"Genetic sequencing and biochemical profiling (methylmalonic aciduria, lactic acidosis, mtDNA depletion) in affected patients","pmids":["19526370"],"confidence":"Medium","gaps":["Single case report; functional consequences of mutation not directly tested in cell-based assays","No enzyme activity measurement performed"]},{"year":2010,"claim":"Demonstrating that SUCLG1 is required to stabilize the SUCLA2 beta subunit: it was unclear whether the alpha subunit was structurally necessary for beta subunit integrity; western blotting of SUCLG1-null fibroblasts showed complete loss of SUCLA2, establishing obligate heterodimer stabilization.","evidence":"Western blot of patient fibroblasts lacking SUCLG1 protein; minigene expression system confirming splicing mutation","pmids":["20693550"],"confidence":"High","gaps":["Did not test SUCLG2 stability independently","Mechanism of beta subunit degradation (proteasomal vs. other) not identified"]},{"year":2016,"claim":"Proving SUCLG1 is necessary and sufficient for SCS activity, mtDNA maintenance, and respiration: rescue of all three phenotypes by ectopic wild-type SUCLG1 in patient cells established a direct causal chain from SUCLG1 loss to TCA cycle dysfunction and mtDNA depletion.","evidence":"SCS enzyme activity assay, mtDNA quantification, cellular respiration assay, and rescue by ectopic wild-type SUCLG1 in patient fibroblasts","pmids":["27484306"],"confidence":"High","gaps":["Mechanism linking SCS activity loss to mtDNA depletion (nucleotide pool vs. other) not resolved","In vivo rescue not performed"]},{"year":2018,"claim":"Extending the alpha subunit's stabilizing role to SUCLG2 and linking SUCLG1 loss to mitochondrial fragmentation: prior work addressed SUCLA2 stability; here, a pathogenic SUCLG1 missense mutation was shown to also deplete SUCLG2 protein and cause its mislocalization, while inducing mitochondrial fragmentation independent of ETC activity or mtDNA copy number changes.","evidence":"Enzyme activity assay for substrate-level phosphorylation, immunoblot, confocal immunocytochemistry, and respirometry in patient fibroblasts","pmids":["30470562"],"confidence":"High","gaps":["Mechanism by which SUCLG1 loss causes mitochondrial fragmentation is unknown","Whether SUCLG2 mislocalization is cause or consequence of fragmentation is unresolved"]},{"year":2024,"claim":"Revealing a non-catalytic signaling role for SUCLG1 through metabolite-mediated post-translational modification: it was unknown how TCA cycle enzymes could regulate mitochondrial gene expression; SUCLG1 was shown to restrict succinyl-CoA levels, preventing succinylation of POLRMT at K622, thereby preserving POLRMT–mtDNA interactions and mtDNA transcription, with FLT3-mutant leukemias exploiting SUCLG1 upregulation to enhance mitochondrial biogenesis.","evidence":"Succinylation proteomics, K622 site-directed mutagenesis, Co-IP of POLRMT with mtDNA/transcription factors, SUCLG1/POLRMT genetic depletion in mouse and humanized leukemia models, succinyl-CoA measurement in clinical samples","pmids":["38649537"],"confidence":"High","gaps":["Whether POLRMT K622 succinylation is regulated in non-leukemic contexts is unknown","Other succinylation targets controlled by SUCLG1-dependent succinyl-CoA flux not systematically defined"]},{"year":2025,"claim":"Demonstrating SUCLG1 promotes mitochondrial fusion and aerobic respiration in a tumor context: loss- and gain-of-function experiments in plexiform neurofibroma cells showed SUCLG1 drives mitochondrial fusion, enhances oxidative phosphorylation, and promotes cell proliferation and migration.","evidence":"SUCLG1 knockdown and overexpression, Seahorse metabolic flux assay, electron microscopy, flow cytometry, qPCR and western blot in neurofibroma cell lines","pmids":["39749698"],"confidence":"Medium","gaps":["Whether the pro-fusion role is direct or secondary to TCA cycle metabolite changes is unknown","Mechanism linking SUCLG1 to SLC25A1 upregulation not established","Single tumor type studied"]},{"year":2026,"claim":"Identifying post-translational regulation of SUCLG1 enzymatic activity by butyrylation: it was unknown how SUCLG1 activity is modulated beyond substrate availability; proteomic screening revealed butyrylation at K90 impairs SUCLG1 catalytic function, and SIRT4 was identified as the debutyrylase responsible for removing this modification.","evidence":"Butyrylome proteomic screening, SIRT4 inhibitor and overexpression experiments, in vivo mouse HFpEF model and phenylephrine-treated cellular model","pmids":["41991142"],"confidence":"Medium","gaps":["Whether K90 butyrylation affects SUCLG1 interactions with beta subunits is untested","In vitro reconstitution of SIRT4-mediated debutyrylation of SUCLG1 not shown"]},{"year":null,"claim":"The mechanism by which SUCLG1/SCS activity loss leads to mtDNA depletion remains unresolved — whether this occurs via disrupted mitochondrial nucleotide salvage (NDPK interaction), altered succinyl-CoA signaling, or another pathway is not definitively established.","evidence":"","pmids":[],"confidence":"Low","gaps":["No direct demonstration of mechanism linking SCS catalysis to mtDNA copy number","Structural basis for beta subunit stabilization by SUCLG1 not determined","Tissue-specific roles of SUCLG1 (brain vs. muscle vs. hematopoietic) not systematically compared"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,1,2,6]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,1,2,3]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[2,3,6]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[3,4]}],"complexes":["Succinate-CoA ligase (SCS/SUCL)"],"partners":["SUCLA2","SUCLG2","POLRMT","SIRT4"],"other_free_text":[]},"mechanistic_narrative":"SUCLG1 encodes the alpha subunit of mitochondrial succinate-CoA ligase (SUCL), a heterodimeric TCA cycle enzyme that catalyzes substrate-level phosphorylation and is essential for mtDNA maintenance, mitochondrial respiration, and mitochondrial morphology. SUCLG1 is required to stabilize both beta subunit isoforms (SUCLA2 and SUCLG2); its absence leads to degradation or mislocalization of these partners, loss of SCS activity, mtDNA depletion, and impaired respiration, all of which are rescued by ectopic SUCLG1 expression [PMID:20693550, PMID:27484306, PMID:30470562]. Beyond its catalytic role, SUCLG1 controls succinyl-CoA levels to suppress succinylation of mitochondrial RNA polymerase (POLRMT) at K622, thereby maintaining POLRMT–mtDNA interactions, mtDNA transcription, and mitochondrial biogenesis; this axis is co-opted by FLT3-mutant leukemias to enhance mitobiogenesis and disease progression [PMID:38649537]. Biallelic loss-of-function mutations in SUCLG1 cause encephalomyopathic mtDNA depletion syndrome with methylmalonic aciduria [PMID:19526370, PMID:27484306]."},"prefetch_data":{"uniprot":{"accession":"P53597","full_name":"Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial","aliases":["Itaconyl--CoA ligase [ADP/GDP-forming] subunit alpha","Malyl--CoA ligase [ADP/GDP-forming] subunit alpha","Succinyl-CoA synthetase subunit alpha","SCS-alpha"],"length_aa":346,"mass_kda":36.2,"function":"Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA (PubMed:34492704, PubMed:40108300). The alpha subunit of the enzyme binds the substrates coenzyme A and phosphate, while succinate binding and specificity for either ATP or GTP is provided by different beta subunits (By similarity). Also able to act as an itaconyl- and malyl-CoA synthetase (PubMed:40108300)","subcellular_location":"Mitochondrion","url":"https://www.uniprot.org/uniprotkb/P53597/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SUCLG1","classification":"Not Classified","n_dependent_lines":83,"n_total_lines":1208,"dependency_fraction":0.06870860927152318},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SUCLG1","total_profiled":1310},"omim":[{"mim_id":"612073","title":"MITOCHONDRIAL DNA DEPLETION SYNDROME 5 (ENCEPHALOMYOPATHIC WITH OR WITHOUT METHYLMALONIC ACIDURIA); MTDPS5","url":"https://www.omim.org/entry/612073"},{"mim_id":"611224","title":"SUCCINATE-CoA LIGASE, GDP/ADP-FORMING, SUBUNIT ALPHA; SUCLG1","url":"https://www.omim.org/entry/611224"},{"mim_id":"603922","title":"SUCCINATE-CoA LIGASE, GDP-FORMING, SUBUNIT BETA; SUCLG2","url":"https://www.omim.org/entry/603922"},{"mim_id":"603921","title":"SUCCINATE-CoA LIGASE, ADP-FORMING, SUBUNIT BETA; SUCLA2","url":"https://www.omim.org/entry/603921"},{"mim_id":"603041","title":"MITOCHONDRIAL DNA DEPLETION SYNDROME 1 (MNGIE TYPE); MTDPS1","url":"https://www.omim.org/entry/603041"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Mitochondria","reliability":"Approved"},{"location":"Plasma membrane","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"kidney","ntpm":516.6}],"url":"https://www.proteinatlas.org/search/SUCLG1"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"P53597","domains":[{"cath_id":"3.40.50.720","chopping":"47-172","consensus_level":"medium","plddt":98.5886,"start":47,"end":172},{"cath_id":"3.40.50.261","chopping":"191-346","consensus_level":"medium","plddt":97.7631,"start":191,"end":346}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P53597","model_url":"https://alphafold.ebi.ac.uk/files/AF-P53597-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P53597-F1-predicted_aligned_error_v6.png","plddt_mean":91.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SUCLG1","jax_strain_url":"https://www.jax.org/strain/search?query=SUCLG1"},"sequence":{"accession":"P53597","fasta_url":"https://rest.uniprot.org/uniprotkb/P53597.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P53597/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P53597"}},"corpus_meta":[{"pmid":"26475597","id":"PMC_26475597","title":"Succinate-CoA ligase deficiency due to mutations in SUCLA2 and SUCLG1: phenotype and genotype correlations in 71 patients.","date":"2015","source":"Journal of inherited metabolic disease","url":"https://pubmed.ncbi.nlm.nih.gov/26475597","citation_count":71,"is_preprint":false},{"pmid":"20693550","id":"PMC_20693550","title":"The severity of phenotype linked to SUCLG1 mutations could be correlated with residual amount of SUCLG1 protein.","date":"2010","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/20693550","citation_count":41,"is_preprint":false},{"pmid":"19526370","id":"PMC_19526370","title":"A novel missense mutation in SUCLG1 associated with mitochondrial DNA depletion, encephalomyopathic form, with methylmalonic aciduria.","date":"2009","source":"European journal of pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/19526370","citation_count":41,"is_preprint":false},{"pmid":"20197121","id":"PMC_20197121","title":"New SUCLG1 patients expanding the phenotypic spectrum of this rare cause of mild methylmalonic aciduria.","date":"2010","source":"Mitochondrion","url":"https://pubmed.ncbi.nlm.nih.gov/20197121","citation_count":33,"is_preprint":false},{"pmid":"38649537","id":"PMC_38649537","title":"SUCLG1 restricts POLRMT succinylation to enhance mitochondrial biogenesis and leukemia progression.","date":"2024","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/38649537","citation_count":27,"is_preprint":false},{"pmid":"20227526","id":"PMC_20227526","title":"Marked mitochondrial DNA depletion associated with a novel SUCLG1 gene mutation resulting in lethal neonatal acidosis, multi-organ failure, and interrupted aortic arch.","date":"2010","source":"Mitochondrion","url":"https://pubmed.ncbi.nlm.nih.gov/20227526","citation_count":26,"is_preprint":false},{"pmid":"30470562","id":"PMC_30470562","title":"Mutated SUCLG1 causes mislocalization of SUCLG2 protein, morphological alterations of mitochondria and an early-onset severe neurometabolic disorder.","date":"2018","source":"Molecular genetics and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/30470562","citation_count":25,"is_preprint":false},{"pmid":"21639866","id":"PMC_21639866","title":"Neonatal lactic acidosis with methylmalonic aciduria due to novel mutations in the SUCLG1 gene.","date":"2011","source":"Pediatrics international : official journal of the Japan Pediatric Society","url":"https://pubmed.ncbi.nlm.nih.gov/21639866","citation_count":20,"is_preprint":false},{"pmid":"27484306","id":"PMC_27484306","title":"Expanding the phenotypic spectrum of Succinyl-CoA ligase deficiency through functional validation of a new SUCLG1 variant.","date":"2016","source":"Molecular genetics and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/27484306","citation_count":16,"is_preprint":false},{"pmid":"27896121","id":"PMC_27896121","title":"A SUCLG1 mutation in a patient with mitochondrial DNA depletion and congenital anomalies.","date":"2014","source":"Molecular genetics and metabolism reports","url":"https://pubmed.ncbi.nlm.nih.gov/27896121","citation_count":15,"is_preprint":false},{"pmid":"21093335","id":"PMC_21093335","title":"Fatal infantile lactic acidosis and a novel homozygous mutation in the SUCLG1 gene: a mitochondrial DNA depletion disorder.","date":"2010","source":"Molecular genetics and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/21093335","citation_count":15,"is_preprint":false},{"pmid":"33230783","id":"PMC_33230783","title":"SUCLG1 mutations and mitochondrial encephalomyopathy: a case study and review of the literature.","date":"2020","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/33230783","citation_count":10,"is_preprint":false},{"pmid":"26028457","id":"PMC_26028457","title":"Five novel SUCLG1 mutations in three Chinese patients with succinate-CoA ligase deficiency noticed by mild methylmalonic aciduria.","date":"2015","source":"Brain & development","url":"https://pubmed.ncbi.nlm.nih.gov/26028457","citation_count":10,"is_preprint":false},{"pmid":"29217198","id":"PMC_29217198","title":"Clinical, Molecular, and Computational Analysis in two cases with mitochondrial encephalomyopathy associated with SUCLG1 mutation in a consanguineous family.","date":"2017","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/29217198","citation_count":9,"is_preprint":false},{"pmid":"35762302","id":"PMC_35762302","title":"Novel compound heterozygous SUCLG1 variants may contribute to mitochondria DNA depletion syndrome-9.","date":"2022","source":"Molecular genetics & genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35762302","citation_count":5,"is_preprint":false},{"pmid":"39749698","id":"PMC_39749698","title":"SUCLG1 promotes aerobic respiration and progression in plexiform neurofibroma.","date":"2025","source":"International journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/39749698","citation_count":2,"is_preprint":false},{"pmid":"39941711","id":"PMC_39941711","title":"Downregulation of Aging-Associated Gene SUCLG1 Marks the Aggressiveness of Liver Disease.","date":"2025","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/39941711","citation_count":2,"is_preprint":false},{"pmid":"38724759","id":"PMC_38724759","title":"A succinylation switch to maligancy: SUCLG1, mitochondrial transcription and leukemia.","date":"2024","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/38724759","citation_count":2,"is_preprint":false},{"pmid":"41991142","id":"PMC_41991142","title":"SIRT4-mediated debutyrylation of SUCLG1 rescues myocardial energy failure in HFpEF: Ginsenoside Rb3 as a novel SIRT4-interacting regulator.","date":"2026","source":"Pharmacological research","url":"https://pubmed.ncbi.nlm.nih.gov/41991142","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.05.29.656916","title":"Reverse remodelling of the mitochondria and cytoskeleton after respiratory heart rate variability pacing of the failing sheep heart","date":"2025-05-30","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.29.656916","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10969,"output_tokens":2026,"usd":0.031649},"stage2":{"model":"claude-opus-4-6","input_tokens":5298,"output_tokens":2380,"usd":0.128985},"total_usd":0.160634,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"SUCLG1 encodes the alpha subunit of succinate-CoA ligase (SUCL), a heterodimeric mitochondrial enzyme; when SUCLG1 protein is absent, SUCLA2 protein is also absent in fibroblasts, indicating that SUCLG1 (alpha subunit) is required to stabilize the SUCLA2 (beta subunit) heterodimer partner, preventing its degradation.\",\n      \"method\": \"Western blot analysis of patient fibroblasts lacking SUCLG1 protein; minigene expression system to confirm splicing mutation\",\n      \"journal\": \"Journal of medical genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal western blot in patient cells, replicated across multiple subsequent studies\",\n      \"pmids\": [\"20693550\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Mutated SUCLG1 (p.Ala209Glu) causes loss of SUCLG1 protein, severely reduced SUCLA2 and SUCLG2 protein levels, impaired mitochondrial substrate-level phosphorylation (mSLP), mislocalization of SUCLG2 away from the mitochondrial network, and increased mitochondrial fragmentation, without changes in ETC activities or mtDNA levels.\",\n      \"method\": \"Enzyme activity assay for mSLP, immunoblot analysis, confocal triple immunocytochemistry, oxygen consumption and extracellular acidification rate measurements in skin fibroblasts\",\n      \"journal\": \"Molecular genetics and metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (enzyme assay, imaging, respirometry) in patient-derived cells, single lab\",\n      \"pmids\": [\"30470562\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Loss of SUCLG1 protein leads to loss of SCS enzyme activity, mtDNA depletion, and cellular respiration defects; ectopic expression of wild-type SUCLG1 in patient fibroblasts rescues all these phenotypes, confirming SUCLG1 is required for SCS activity, mtDNA maintenance, and mitochondrial respiration.\",\n      \"method\": \"SCS enzyme activity assay, mtDNA quantification, cellular respiration assay, rescue by ectopic wild-type SUCLG1 expression in patient fibroblasts\",\n      \"journal\": \"Molecular genetics and metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — rescue experiment with multiple functional readouts, single lab\",\n      \"pmids\": [\"27484306\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SUCLG1 restricts succinyl-CoA levels to suppress succinylation of mitochondrial RNA polymerase (POLRMT) at lysine 622; this hyposuccinylation maintains POLRMT interaction with mtDNA and mitochondrial transcription factors, preserving mtDNA transcription and mitochondrial biogenesis. FLT3 mutations upregulate SUCLG1 expression to reduce succinyl-CoA and POLRMT succinylation, enhancing mitobiogenesis and leukemia progression.\",\n      \"method\": \"Succinylation proteomics, site-directed mutagenesis (K622 succinylation site), Co-IP of POLRMT with mtDNA/transcription factors, genetic depletion of SUCLG1 and POLRMT in mouse and humanized leukemia models, succinyl-CoA level measurement in clinical samples\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods including mutagenesis, Co-IP, in vivo models, and clinical validation\",\n      \"pmids\": [\"38649537\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"SUCLG1 encodes the alpha subunit of succinate-CoA ligase; missense mutations in SUCLG1 cause the encephalomyopathic mtDNA depletion syndrome with methylmalonic aciduria, phenotypically similar to SUCLA2 mutations.\",\n      \"method\": \"Genetic sequencing, clinical biochemical profiling (methylmalonic aciduria, lactic acidosis), mtDNA quantification\",\n      \"journal\": \"European journal of pediatrics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — genetic and biochemical characterization, single case report\",\n      \"pmids\": [\"19526370\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The p.M14T mutation in SUCLG1 is located in the mitochondrial targeting sequence; in-silico analysis predicted this mutation alters protein stability and mitochondrial translocation, and patients showed decreased mtDNA copy number.\",\n      \"method\": \"Mutational analysis, in-silico structural prediction, real-time PCR for mtDNA quantification\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 — primarily computational prediction with indirect functional evidence (mtDNA depletion)\",\n      \"pmids\": [\"29217198\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"SUCLG1 is butyrylated at K90 in the context of HFpEF, which impairs its enzymatic function in the TCA cycle, reducing succinate and ATP production; SIRT4 acts as a debutyrylase for SUCLG1, and reduced SIRT4 expression leads to SUCLG1 hyperbutyrylation and impaired enzymatic activity.\",\n      \"method\": \"Butyrylome proteomic screening, SIRT4 inhibitor and overexpression experiments, in vivo mouse HFpEF model, cellular model with phenylephrine\",\n      \"journal\": \"Pharmacological research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — proteomic identification + genetic manipulation (overexpression/inhibitor) with functional enzymatic readout, single lab\",\n      \"pmids\": [\"41991142\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SUCLG1 promotes mitochondrial fusion and enhances aerobic respiration (without affecting glycolysis) in plexiform neurofibroma cells; SUCLG1 knockdown reduces proliferation and migration, while overexpression enhances these processes and upregulates SLC25A1 expression.\",\n      \"method\": \"SUCLG1 knockdown and overexpression, Seahorse assay for aerobic respiration and glycolysis, electron microscopy of mitochondria, flow cytometry, qPCR and western blot\",\n      \"journal\": \"International journal of oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss- and gain-of-function with multiple orthogonal functional readouts, single lab\",\n      \"pmids\": [\"39749698\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SUCLG1 encodes the alpha subunit of mitochondrial succinate-CoA ligase (SUCL), which is essential for TCA cycle substrate-level phosphorylation, mtDNA maintenance, and stabilization of the beta subunits SUCLA2 and SUCLG2; additionally, SUCLG1 controls succinyl-CoA levels to suppress succinylation of mitochondrial RNA polymerase (POLRMT) at K622, thereby maintaining mtDNA transcription and mitochondrial biogenesis, while its enzymatic activity is itself regulated by post-translational modifications including butyrylation at K90 (removed by SIRT4).\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SUCLG1 encodes the alpha subunit of mitochondrial succinate-CoA ligase (SUCL), a heterodimeric TCA cycle enzyme that catalyzes substrate-level phosphorylation and is essential for mtDNA maintenance, mitochondrial respiration, and mitochondrial morphology. SUCLG1 is required to stabilize both beta subunit isoforms (SUCLA2 and SUCLG2); its absence leads to degradation or mislocalization of these partners, loss of SCS activity, mtDNA depletion, and impaired respiration, all of which are rescued by ectopic SUCLG1 expression [PMID:20693550, PMID:27484306, PMID:30470562]. Beyond its catalytic role, SUCLG1 controls succinyl-CoA levels to suppress succinylation of mitochondrial RNA polymerase (POLRMT) at K622, thereby maintaining POLRMT–mtDNA interactions, mtDNA transcription, and mitochondrial biogenesis; this axis is co-opted by FLT3-mutant leukemias to enhance mitobiogenesis and disease progression [PMID:38649537]. Biallelic loss-of-function mutations in SUCLG1 cause encephalomyopathic mtDNA depletion syndrome with methylmalonic aciduria [PMID:19526370, PMID:27484306].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Establishing that SUCLG1 is a disease gene: before this, the genetic basis of some encephalomyopathic mtDNA depletion cases was unknown; identification of biallelic SUCLG1 mutations linked the alpha subunit to a Mendelian mtDNA depletion syndrome with methylmalonic aciduria, paralleling SUCLA2-associated disease.\",\n      \"evidence\": \"Genetic sequencing and biochemical profiling (methylmalonic aciduria, lactic acidosis, mtDNA depletion) in affected patients\",\n      \"pmids\": [\"19526370\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single case report; functional consequences of mutation not directly tested in cell-based assays\", \"No enzyme activity measurement performed\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Demonstrating that SUCLG1 is required to stabilize the SUCLA2 beta subunit: it was unclear whether the alpha subunit was structurally necessary for beta subunit integrity; western blotting of SUCLG1-null fibroblasts showed complete loss of SUCLA2, establishing obligate heterodimer stabilization.\",\n      \"evidence\": \"Western blot of patient fibroblasts lacking SUCLG1 protein; minigene expression system confirming splicing mutation\",\n      \"pmids\": [\"20693550\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not test SUCLG2 stability independently\", \"Mechanism of beta subunit degradation (proteasomal vs. other) not identified\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Proving SUCLG1 is necessary and sufficient for SCS activity, mtDNA maintenance, and respiration: rescue of all three phenotypes by ectopic wild-type SUCLG1 in patient cells established a direct causal chain from SUCLG1 loss to TCA cycle dysfunction and mtDNA depletion.\",\n      \"evidence\": \"SCS enzyme activity assay, mtDNA quantification, cellular respiration assay, and rescue by ectopic wild-type SUCLG1 in patient fibroblasts\",\n      \"pmids\": [\"27484306\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking SCS activity loss to mtDNA depletion (nucleotide pool vs. other) not resolved\", \"In vivo rescue not performed\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extending the alpha subunit's stabilizing role to SUCLG2 and linking SUCLG1 loss to mitochondrial fragmentation: prior work addressed SUCLA2 stability; here, a pathogenic SUCLG1 missense mutation was shown to also deplete SUCLG2 protein and cause its mislocalization, while inducing mitochondrial fragmentation independent of ETC activity or mtDNA copy number changes.\",\n      \"evidence\": \"Enzyme activity assay for substrate-level phosphorylation, immunoblot, confocal immunocytochemistry, and respirometry in patient fibroblasts\",\n      \"pmids\": [\"30470562\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which SUCLG1 loss causes mitochondrial fragmentation is unknown\", \"Whether SUCLG2 mislocalization is cause or consequence of fragmentation is unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealing a non-catalytic signaling role for SUCLG1 through metabolite-mediated post-translational modification: it was unknown how TCA cycle enzymes could regulate mitochondrial gene expression; SUCLG1 was shown to restrict succinyl-CoA levels, preventing succinylation of POLRMT at K622, thereby preserving POLRMT–mtDNA interactions and mtDNA transcription, with FLT3-mutant leukemias exploiting SUCLG1 upregulation to enhance mitochondrial biogenesis.\",\n      \"evidence\": \"Succinylation proteomics, K622 site-directed mutagenesis, Co-IP of POLRMT with mtDNA/transcription factors, SUCLG1/POLRMT genetic depletion in mouse and humanized leukemia models, succinyl-CoA measurement in clinical samples\",\n      \"pmids\": [\"38649537\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether POLRMT K622 succinylation is regulated in non-leukemic contexts is unknown\", \"Other succinylation targets controlled by SUCLG1-dependent succinyl-CoA flux not systematically defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrating SUCLG1 promotes mitochondrial fusion and aerobic respiration in a tumor context: loss- and gain-of-function experiments in plexiform neurofibroma cells showed SUCLG1 drives mitochondrial fusion, enhances oxidative phosphorylation, and promotes cell proliferation and migration.\",\n      \"evidence\": \"SUCLG1 knockdown and overexpression, Seahorse metabolic flux assay, electron microscopy, flow cytometry, qPCR and western blot in neurofibroma cell lines\",\n      \"pmids\": [\"39749698\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the pro-fusion role is direct or secondary to TCA cycle metabolite changes is unknown\", \"Mechanism linking SUCLG1 to SLC25A1 upregulation not established\", \"Single tumor type studied\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identifying post-translational regulation of SUCLG1 enzymatic activity by butyrylation: it was unknown how SUCLG1 activity is modulated beyond substrate availability; proteomic screening revealed butyrylation at K90 impairs SUCLG1 catalytic function, and SIRT4 was identified as the debutyrylase responsible for removing this modification.\",\n      \"evidence\": \"Butyrylome proteomic screening, SIRT4 inhibitor and overexpression experiments, in vivo mouse HFpEF model and phenylephrine-treated cellular model\",\n      \"pmids\": [\"41991142\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether K90 butyrylation affects SUCLG1 interactions with beta subunits is untested\", \"In vitro reconstitution of SIRT4-mediated debutyrylation of SUCLG1 not shown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The mechanism by which SUCLG1/SCS activity loss leads to mtDNA depletion remains unresolved — whether this occurs via disrupted mitochondrial nucleotide salvage (NDPK interaction), altered succinyl-CoA signaling, or another pathway is not definitively established.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct demonstration of mechanism linking SCS catalysis to mtDNA copy number\", \"Structural basis for beta subunit stabilization by SUCLG1 not determined\", \"Tissue-specific roles of SUCLG1 (brain vs. muscle vs. hematopoietic) not systematically compared\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 1, 2, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 1, 2, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [2, 3, 6]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"complexes\": [\n      \"Succinate-CoA ligase (SCS/SUCL)\"\n    ],\n    \"partners\": [\n      \"SUCLA2\",\n      \"SUCLG2\",\n      \"POLRMT\",\n      \"SIRT4\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}