{"gene":"YME1L1","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2007,"finding":"YME1L (Yme1L) is the protease responsible for OPA1 cleavage at site S2 in the mitochondrial inner membrane. Loss of membrane potential destabilizes OPA1 long isoforms and enhances cleavage at S1 (but not S2), while S2 cleavage is specifically regulated by Yme1L.","method":"Cellular reconstitution in OPA1-null cells; shRNA knockdown of Yme1L; analysis of OPA1 isoform patterns by western blot","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean loss-of-function in defined null background, replicated across multiple labs subsequently","pmids":["17709429"],"is_preprint":false},{"year":2012,"finding":"Human YME1L is an integral inner mitochondrial membrane protein that exposes its carboxy-terminus to the intermembrane space and exists in large complexes of 600–1100 kDa. Its proteolytic activity is required for degrading non-assembled respiratory chain subunits (Ndufb6, ND1, Cox4), maintaining cristae morphology, supporting cell proliferation, and conferring apoptotic resistance.","method":"Stable shRNA knockdown in HEK293 cells; rescue with wild-type vs. proteolytically inactive YME1L mutant; electron microscopy; western blot; respiration assay","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Moderate — KO/rescue with catalytic mutant and multiple orthogonal readouts in single lab","pmids":["22262461"],"is_preprint":false},{"year":2014,"finding":"YME1L performs constitutive cleavage of OPA1, and together with OMA1 generates both long and short OPA1 forms that maintain mitochondrial fusion. Short OPA1 forms produced by OMA1/YME1L processing promote mitochondrial fission and partially co-localize with ER-mitochondria contact sites and the fission machinery. Long OPA1 forms alone are sufficient to mediate fusion in the absence of both YME1L and OMA1.","method":"Genetic deletion of Yme1l, Oma1, or both; mitochondrial morphology imaging; epistasis analysis; co-localization of GTPase-inactive short OPA1 with fission machinery","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — double KO epistasis, replicated and extended by multiple subsequent labs","pmids":["24616225"],"is_preprint":false},{"year":2013,"finding":"Endogenous Yme1L localizes to punctate structures on mitochondria. Loss of Yme1L causes mitochondrial fragmentation through increased Drp1 recruitment (via elevated MiD49/Mff), not via OPA1 S1/S2 processing; shYme1L stabilizes L-OPA1 and exogenous OPA1/L-OPA1 further promotes fragmentation. SLP-2 interacts with Yme1L. Loss of Drp1 or Mff rescues shYme1L-induced fragmentation.","method":"shRNA knockdown in MEF cells; live-cell mitochondrial dynamics imaging; co-immunoprecipitation of SLP-2 with Yme1L; epistasis with Drp1/Mff KO","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — single lab, multiple orthogonal methods including live imaging and epistasis","pmids":["24176854"],"is_preprint":false},{"year":2016,"finding":"SLP2 anchors a large protease complex (SPY complex) at the mitochondrial inner membrane comprising PARL and YME1L. Association with SLP2 regulates PARL-mediated processing of PINK1 and PGAM5, and SLP2 inhibits OMA1-mediated OPA1 cleavage, thereby enabling stress-induced mitochondrial hyperfusion. SLP2 restricts OMA1 activity by direct binding.","method":"Co-immunoprecipitation; blue-native PAGE complex analysis; genetic deletion/knockdown of SLP2; processing assays for PINK1, PGAM5, OPA1; mitochondrial morphology imaging under starvation stress","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, multiple substrate processing assays, genetic KO with functional rescue in single thorough study","pmids":["27737933"],"is_preprint":false},{"year":2016,"finding":"A homozygous missense mutation in the mitochondrial pre-sequence of YME1L1 inhibits its cleavage by the mitochondrial processing peptidase (MPP), leading to rapid degradation of the YME1L1 precursor protein. This abolishes YME1L1 function, causes abnormal OPA1 processing, mitochondrial network fragmentation, and a proliferation defect in patient-derived cells.","method":"Patient fibroblast studies; western blot for precursor vs. mature YME1L1; OPA1 isoform analysis; mitochondrial morphology imaging; genetic complementation","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Moderate — human disease variant functionally validated with multiple orthogonal assays in patient-derived cells","pmids":["27495975"],"is_preprint":false},{"year":2018,"finding":"ROMO1 is a constituent of the human TIM23 presequence translocase that is specifically required for import of YME1L into the inner mitochondrial membrane. Loss of ROMO1 causes selective loss of YME1L (but not general presequence import), leading to aberrant OPA1 processing and inner membrane structural defects. This selective requirement is linked to the unusually long and charge-distributed targeting sequence of YME1L.","method":"Mass spectrometry identification of TIM23 complex components; ROMO1 knockout cell line; quantitative proteomics; protein import assays; OPA1 processing assay; inner membrane morphology by EM","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — MS-defined complex, KO cell line, import assay with defined mechanistic link to YME1L targeting sequence","pmids":["30598479"],"is_preprint":false},{"year":2019,"finding":"YME1L rewires the mitochondrial proteome in response to hypoxia or nutrient starvation via a lipid signalling cascade. Inhibition of mTORC1 activates LIPIN1 phosphatidic acid phosphatase, which decreases mitochondrial phosphatidylethanolamine levels and promotes YME1L-mediated proteolysis of mitochondrial protein translocases, lipid transfer proteins, and metabolic enzymes, acutely limiting mitochondrial biogenesis while supporting cell growth.","method":"Quantitative mitochondrial proteomics under hypoxia/starvation; mTORC1 inhibition; LIPIN1 genetic manipulation; lipid mass spectrometry for PE levels; YME1L KO; xenograft tumor models","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (proteomics, lipidomics, genetics, in vivo), rigorous mechanistic pathway dissection","pmids":["31695197"],"is_preprint":false},{"year":2019,"finding":"YME1L-deficient mice lacking YME1L in the nervous system develop ocular dysfunction and selective degeneration of spinal cord proprioceptive axons. Deletion of Oma1 in Yme1l-null mice restores tubular mitochondria but worsens axonal degeneration, establishing that impaired mitochondrial proteostasis (not mitochondrial fragmentation per se) causes the neurological defects.","method":"Conditional nervous-system-specific Yme1l KO mice; double Yme1l/Oma1 KO epistasis; histological and behavioral analysis; mitochondrial morphology imaging","journal":"EMBO molecular medicine","confidence":"High","confidence_rationale":"Tier 2 / Moderate — in vivo conditional KO with double-KO epistasis dissecting fragmentation from proteostasis roles","pmids":["30389680"],"is_preprint":false},{"year":2019,"finding":"KIF1Bβ physically interacts with YME1L1 through its death-inducing region and stimulates YME1L1 protease activity to cleave long OPA1 forms, causing mitochondrial fragmentation and apoptosis. Both KIF1Bβ and YME1L1 are upregulated upon NGF withdrawal in PC12 cells, and knockdown of either protein inhibits NGF-depletion-induced apoptosis.","method":"Co-immunoprecipitation of KIF1Bβ with YME1L1; domain-mapping with deletion constructs; OPA1 cleavage assay; siRNA knockdown of each protein; NGF-withdrawal apoptosis model","journal":"Molecular carcinogenesis","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single lab, Co-IP plus functional assay but no in vitro reconstitution of stimulated protease activity","pmids":["30859632"],"is_preprint":false},{"year":2019,"finding":"Loss of Yme1L in C2C12 myotubes activates AMPK and FoxO3a and increases expression of MuRF1 and myostatin, contributing to muscle atrophy. Yme1L depletion causes accumulation of short OPA1 forms and mitochondrial fragmentation, and this effect is specific to Yme1L (not LonP1).","method":"shRNA knockdown of Yme1L in C2C12 myotubes; hindlimb-immobilized mouse model; western blot for OPA1 isoforms, AMPK, FoxO3a, MuRF1, myostatin; mitochondrial morphology","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, defined cellular phenotype with pathway markers but no reconstitution or epistasis for pathway placement","pmids":["31725201"],"is_preprint":false},{"year":2020,"finding":"ATP binding stabilizes the hexameric structure of the YME1L catalytic domain and protects it from urea-induced unfolding and loss of active hexamers, as measured by fluorescence unfolding and stopped-flow nucleotide-binding assays.","method":"Protein unfolding fluorescence assay with urea; stopped-flow fluorescence for nucleotide binding and unfoldase activity; multiple fluorophore systems","journal":"Biomolecules","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro biochemical assay on purified protein but single lab, single study","pmids":["32340357"],"is_preprint":false},{"year":2022,"finding":"YME1L controls the abundance of numerous mitochondrial substrates in quiescent neural stem and progenitor cells (NSPCs). Conditional Yme1l deletion activates a differentiation program with broad metabolic changes, irreversibly shifting NSPCs away from a fatty-acid-oxidation-dependent state and causing premature differentiation and NSPC pool depletion in vivo.","method":"Conditional Yme1l KO in adult NSPCs in vivo; quantitative mitochondrial proteomics; metabolic profiling; fate-mapping and self-renewal assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — in vivo conditional KO with proteomics and metabolic phenotyping, multiple orthogonal readouts","pmids":["35172139"],"is_preprint":false},{"year":2022,"finding":"Sirt3 deacetylates YME1L1, and this deacetylation promotes OPA1-mediated mitochondrial fusion. Loss of Sirt3 increases YME1L1 acetylation and impairs fusion; Sirt3 overexpression rescues LPS-induced mitochondrial damage and apoptosis in renal tubular epithelial cells via the YME1L1-OPA1 axis.","method":"Sirt3 KO mice + LPS model; Sirt3 overexpression in HK-2 cells; co-immunoprecipitation; deacetylation assay; OPA1 processing analysis; mitochondrial morphology by immunofluorescence and electron microscopy","journal":"Cell proliferation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO mouse plus cellular overexpression, Co-IP for interaction, but acetylation site not mapped by mutagenesis","pmids":["36433732"],"is_preprint":false},{"year":2024,"finding":"Plugging the TOM complex in mammalian cells induces YME1L1-dependent degradation of TIM23 channel components TIMM17A and TIMM23. Unoccupied TIM23 complexes appear to expose a C-terminal degron on TIMM17A that is recognized by YME1L1 for proteolysis. Loss of YME1L1 exacerbates the growth defect caused by TOM channel plugging.","method":"DHFR-MIC60 import-blocking system stabilized by methotrexate; YME1L1 KO cell lines; western blot for TIMM17A/TIMM23 levels; cell growth assays","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — defined genetic system with KO, multiple substrates identified, functional consequence measured","pmids":["39774271"],"is_preprint":false},{"year":2024,"finding":"YME1L1 directly degrades SLC25A38, a short-lived mitochondrial glycine transporter (half-life ~4 h). Pharmacological inhibition or genetic depletion of YME1L1 stabilizes SLC25A38. Depolarization of mitochondrial membrane potential by CCCP prevents SLC25A38 degradation, linking its turnover to inner membrane integrity.","method":"Protein half-life analysis; pharmacological inhibition of proteolytic systems; YME1L1 genetic depletion; CCCP depolarization experiment; western blot for SLC25A38 stability","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic and pharmacological evidence in single preprint, no in vitro reconstitution","pmids":["38979268"],"is_preprint":true},{"year":2024,"finding":"YME1L interacts with BCL2L13 (a mitophagy receptor) and promotes its phosphorylation, thereby enhancing mitophagy in renal tubular epithelial cells. LC-MS/MS identified BCL2L13 as a YME1L-interacting protein.","method":"LC-MS/MS interactome analysis; co-immunoprecipitation; phosphorylation assay; in vivo AAV-mediated YME1L overexpression; mitophagy flux assays","journal":"Biological research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, MS-identified interaction with limited mechanistic follow-up on phosphorylation","pmids":["38494498"],"is_preprint":false},{"year":2025,"finding":"A novel homozygous YME1L1 variant (p.Leu667Val) causes defective proteolytic processing of OPA1 and PRELID1 (PRELI domain containing 1), enhanced mitochondrial fission, attenuated Krebs cycle enzyme activities, and reduced mitochondrial respiration in patient fibroblasts, classifying YME1L1 deficiency as a form of secondary 3-methylglutaconic aciduria.","method":"Patient fibroblast functional studies; OPA1 and PRELID1 processing assays; mitochondrial morphology imaging; Krebs cycle enzyme activity assays; mitochondrial respiration measurement","journal":"Journal of inherited metabolic disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal functional assays in patient-derived cells, single lab","pmids":["40255048"],"is_preprint":false},{"year":2025,"finding":"Nucleotide (ATP) binding reduces backbone flexibility and modulates side-chain dynamics of the AAA+ domain of YME1L, while Zn²⁺ binding stabilizes the protease domain. Long-range allostery between the AAA+ and protease domains is mediated by a critical salt bridge at the inter-domain interface, and disruption of this salt bridge impairs ATP-dependent substrate degradation.","method":"HDX-MS; NMR spectroscopy; site-directed mutagenesis of salt bridge residue; in vitro substrate degradation assay with hexameric soluble YME1L construct","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — Tier 1 methods (HDX-MS, NMR, mutagenesis + in vitro assay) in single preprint, not yet peer-reviewed","pmids":["bio_10.1101_2025.01.30.635686"],"is_preprint":true},{"year":2025,"finding":"GCN5L1 physically associates with YME1L in the mitochondrial intermembrane space and facilitates YME1L-mediated degradation of the MICOS component MIC13, thereby promoting cristae disassembly during obesity. A high-fat diet triggers GCN5L1 accumulation in the intermembrane space, activating this pathway.","method":"Protein interactome analysis (GCN5L1 KO mice); co-immunoprecipitation; MIC13 degradation assay; cristae morphology by EM; metabolic phenotyping of adipose-specific KO mice","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — interactome plus genetic KO with functional substrate (MIC13) degradation assay, single lab","pmids":["40338741"],"is_preprint":false}],"current_model":"YME1L1 is an ATP-dependent i-AAA metalloprotease anchored in the mitochondrial inner membrane with its catalytic domain facing the intermembrane space, where it constitutively cleaves OPA1 at site S2 (together with OMA1 at S1) to generate both long and short OPA1 isoforms that balance mitochondrial fusion and fission; it also performs quality-control proteolysis of non-assembled respiratory chain subunits, mitochondrial translocases (TIMM17A, TIMM23), lipid transfer proteins, metabolic enzymes, and the glycine transporter SLC25A38, with its proteolytic activity allosterically regulated by ATP binding and inter-domain salt-bridge communication, assembled within the SLP2-PARL-YME1L (SPY) scaffold complex, imported into the inner membrane via a ROMO1-dependent TIM23 pathway, and subject to activity modulation by Sirt3-mediated deacetylation and by mTORC1-LIPIN1-driven changes in phosphatidylethanolamine levels."},"narrative":{"mechanistic_narrative":"YME1L1 is an ATP-dependent inner mitochondrial membrane protease that governs mitochondrial morphology and proteostasis by exposing a catalytic domain to the intermembrane space and assembling into large (600–1100 kDa) complexes [PMID:17709429, PMID:22262461]. It constitutively cleaves OPA1 at site S2 and, together with OMA1, generates the balance of long and short OPA1 isoforms that set the equilibrium between mitochondrial fusion and fission [PMID:17709429, PMID:24616225]. Beyond this central dynamics role, YME1L1 performs quality-control proteolysis of a broad substrate set including non-assembled respiratory chain subunits, where this activity maintains cristae morphology, respiration, proliferation, and apoptotic resistance [PMID:22262461], the TIM23 translocase channel components TIMM17A and TIMM23 when their import channel is unoccupied [PMID:39774271], lipid transfer proteins and metabolic enzymes [PMID:31695197], and the MICOS subunit MIC13 [PMID:40338741]. This proteolysis is mobilized as an adaptive program: mTORC1 inhibition activates LIPIN1, lowering mitochondrial phosphatidylethanolamine and triggering YME1L1-mediated remodeling of the mitochondrial proteome to limit biogenesis while supporting growth under hypoxia or starvation [PMID:31695197]. YME1L1 is anchored within the SLP2–PARL–YME1L (SPY) scaffold at the inner membrane [PMID:24176854, PMID:27737933] and is selectively imported through a ROMO1-dependent TIM23 pathway [PMID:30598479]. In vivo, loss of YME1L1 causes neurodegeneration driven by impaired proteostasis rather than fragmentation per se [PMID:30389680] and depletes neural stem/progenitor pools by forcing premature differentiation [PMID:35172139]. Human homozygous YME1L1 mutations that abolish or impair function cause defective OPA1 processing, mitochondrial fragmentation, and a mitochondriopathy classified as a form of secondary 3-methylglutaconic aciduria [PMID:27495975, PMID:40255048].","teleology":[{"year":2007,"claim":"Establishing which protease produces a specific OPA1 isoform answered how a single dynamin-related GTPase is post-translationally diversified to control fusion; YME1L was identified as the S2-cleaving enzyme.","evidence":"shRNA knockdown of Yme1L and OPA1 isoform analysis in OPA1-null reconstituted cells","pmids":["17709429"],"confidence":"High","gaps":["Did not resolve full substrate spectrum beyond OPA1","Did not establish the regulatory inputs controlling S2 cleavage"]},{"year":2012,"claim":"Defining YME1L topology and catalytic requirement showed it is a bona fide proteolytic quality-control enzyme rather than a passive scaffold, linking its activity to respiratory chain integrity and cell survival.","evidence":"shRNA knockdown with wild-type vs. catalytically dead rescue, EM, respiration assays in HEK293","pmids":["22262461"],"confidence":"High","gaps":["Substrate recognition mechanism not defined","Composition of the 600–1100 kDa complexes not resolved"]},{"year":2014,"claim":"Double-knockout epistasis with OMA1 clarified how two proteases jointly set the long/short OPA1 ratio and demonstrated that long OPA1 forms suffice for fusion.","evidence":"Yme1l/Oma1 single and double genetic deletion, morphology imaging, co-localization of short OPA1 with fission machinery","pmids":["24616225"],"confidence":"High","gaps":["Did not establish how cleavage choice between OMA1 and YME1L is partitioned","Stoichiometry of short-OPA1 action at fission sites unresolved"]},{"year":2013,"claim":"Characterizing the SLP-2 interaction and the Drp1/Mff-dependent fragmentation phenotype showed YME1L influences fission through the recruitment machinery, not only via OPA1 processing.","evidence":"shRNA knockdown in MEFs, live imaging, Co-IP of SLP-2, epistasis with Drp1/Mff knockout","pmids":["24176854"],"confidence":"Medium","gaps":["Single lab","Mechanistic link between YME1L loss and elevated MiD49/Mff not defined"]},{"year":2016,"claim":"Identifying the SPY complex placed YME1L within a defined inner-membrane proteolytic scaffold alongside SLP2 and PARL, contextualizing how multiple processing reactions are spatially organized.","evidence":"Reciprocal Co-IP, blue-native PAGE, SLP2 deletion with PINK1/PGAM5/OPA1 processing assays","pmids":["27737933"],"confidence":"High","gaps":["Direct biochemical architecture of the SPY complex not solved","How SLP2 binding modulates YME1L catalysis specifically not dissected"]},{"year":2016,"claim":"A patient pre-sequence mutation that blocks MPP cleavage established YME1L1 as a human disease gene and demonstrated that loss of mature protein recapitulates OPA1 and morphology defects.","evidence":"Patient fibroblast studies, precursor/mature western blot, OPA1 analysis, genetic complementation","pmids":["27495975"],"confidence":"High","gaps":["Full clinical-molecular spectrum not defined from a single family","Tissue-specific vulnerability not explained"]},{"year":2018,"claim":"Discovering the ROMO1-dependent TIM23 import route explained how YME1L is selectively delivered to the inner membrane and why its unusual targeting sequence creates a specific import dependency.","evidence":"MS identification of TIM23 components, ROMO1 KO, import assays, quantitative proteomics, EM","pmids":["30598479"],"confidence":"High","gaps":["Biochemical basis of ROMO1 recognition of the YME1L pre-sequence not solved","Whether other inner-membrane proteins share this route not fully mapped"]},{"year":2019,"claim":"Linking mTORC1–LIPIN1–phosphatidylethanolamine signaling to YME1L proteolysis revealed how the protease acts as an adaptive sensor that remodels the mitochondrial proteome in response to nutrient and oxygen stress.","evidence":"Quantitative proteomics and lipidomics under hypoxia/starvation, mTORC1 inhibition, LIPIN1 manipulation, YME1L KO, xenografts","pmids":["31695197"],"confidence":"High","gaps":["How lowered PE mechanistically activates YME1L not resolved at the molecular level","Substrate selectivity rules under remodeling not defined"]},{"year":2019,"claim":"Nervous-system conditional knockout with Oma1 epistasis separated YME1L's proteostasis function from morphology, showing that proteostatic failure—not fragmentation—drives neurodegeneration.","evidence":"Conditional Yme1l KO mice, Yme1l/Oma1 double KO, histology, behavior, morphology imaging","pmids":["30389680"],"confidence":"High","gaps":["Specific substrate(s) responsible for axonal degeneration not identified","Cell-type basis of proprioceptive selectivity unexplained"]},{"year":2019,"claim":"Identifying KIF1Bβ as a stimulatory binding partner provided a mechanism for inducible YME1L activation during apoptotic signaling.","evidence":"Co-IP, domain mapping, OPA1 cleavage assay, siRNA, NGF-withdrawal apoptosis model in PC12","pmids":["30859632"],"confidence":"Medium","gaps":["No in vitro reconstitution of stimulated protease activity","Single lab"]},{"year":2019,"claim":"Muscle-cell depletion connected YME1L loss to AMPK/FoxO3a-driven atrophy programs, extending its physiological reach to muscle homeostasis.","evidence":"shRNA in C2C12 myotubes, immobilization mouse model, western blots for OPA1/AMPK/FoxO3a/MuRF1/myostatin","pmids":["31725201"],"confidence":"Medium","gaps":["No epistasis to place YME1L upstream of AMPK","Direct substrate driving atrophy not identified"]},{"year":2020,"claim":"Biochemical study of ATP binding showed nucleotide stabilizes the hexameric catalytic assembly, beginning the mechanistic dissection of allosteric control.","evidence":"Urea unfolding fluorescence and stopped-flow nucleotide-binding assays on purified protein","pmids":["32340357"],"confidence":"Medium","gaps":["Single in vitro study","Did not link nucleotide state to substrate processing on membranes"]},{"year":2022,"claim":"Conditional knockout in neural stem/progenitor cells demonstrated YME1L sets a metabolic state required for quiescence, with its loss forcing premature differentiation and pool depletion.","evidence":"In vivo conditional Yme1l KO, mitochondrial proteomics, metabolic profiling, fate-mapping","pmids":["35172139"],"confidence":"High","gaps":["Key substrate controlling the fatty-acid-oxidation state not pinpointed","Reversibility window not defined"]},{"year":2022,"claim":"Identifying Sirt3-mediated deacetylation of YME1L1 established a post-translational regulatory layer coupling NAD+-dependent signaling to mitochondrial fusion.","evidence":"Sirt3 KO mice + LPS, HK-2 overexpression, Co-IP, deacetylation and OPA1 processing assays","pmids":["36433732"],"confidence":"Medium","gaps":["Acetylation site not mapped by mutagenesis","Direct effect of acetylation on catalytic activity not measured biochemically"]},{"year":2024,"claim":"An import-blocking system revealed YME1L1 degrades unoccupied TIM23 channel subunits via an exposed degron, defining a surveillance role over the translocase itself.","evidence":"DHFR-MIC60 import-block, YME1L1 KO cells, western blots for TIMM17A/TIMM23, growth assays","pmids":["39774271"],"confidence":"High","gaps":["Degron sequence not precisely defined","Whether degradation is direct (not via cofactor) not biochemically reconstituted"]},{"year":2024,"claim":"Identifying SLC25A38 as a short-lived YME1L1 substrate linked the protease to control of a mitochondrial glycine transporter and tied turnover to membrane potential.","evidence":"Half-life analysis, pharmacological/genetic YME1L1 depletion, CCCP depolarization, western blot (preprint)","pmids":["38979268"],"confidence":"Medium","gaps":["No in vitro reconstitution of direct cleavage","Preprint, not peer-reviewed"]},{"year":2024,"claim":"A reported interaction with the mitophagy receptor BCL2L13 raised the possibility that YME1L participates in mitophagy regulation.","evidence":"LC-MS/MS interactome, Co-IP, phosphorylation assay, AAV overexpression, mitophagy flux assays","pmids":["38494498"],"confidence":"Low","gaps":["Single lab with limited mechanistic follow-up on the phosphorylation step","Whether the effect requires YME1L catalytic activity not established"]},{"year":2025,"claim":"A second human homozygous variant (p.Leu667Val) expanded the disease phenotype, linking defective OPA1 and PRELID1 processing to impaired Krebs cycle activity and classifying the deficiency within 3-methylglutaconic aciduria.","evidence":"Patient fibroblast OPA1/PRELID1 processing, morphology imaging, Krebs cycle enzyme and respiration assays","pmids":["40255048"],"confidence":"Medium","gaps":["Genotype-phenotype correlation across patients not established","Mechanism linking PRELID1 mis-processing to metabolic defect not dissected"]},{"year":2025,"claim":"Structural-dynamics analysis defined an inter-domain salt bridge mediating AAA+-to-protease allostery, explaining how ATP and Zn2+ binding are communicated to control substrate degradation.","evidence":"HDX-MS, NMR, salt-bridge mutagenesis, in vitro degradation assay with soluble hexameric construct (preprint)","pmids":["bio_10.1101_2025.01.30.635686"],"confidence":"Medium","gaps":["Preprint, not peer-reviewed","Full-length membrane-embedded enzyme not structurally resolved"]},{"year":2025,"claim":"Identifying GCN5L1 as an intermembrane-space partner that promotes YME1L-mediated MIC13 degradation connected the protease to diet-induced cristae remodeling.","evidence":"GCN5L1 KO interactome, Co-IP, MIC13 degradation assay, EM, adipose-specific KO metabolic phenotyping","pmids":["40338741"],"confidence":"Medium","gaps":["Single lab","Direct vs. cofactor-assisted MIC13 cleavage not reconstituted"]},{"year":null,"claim":"How YME1L's substrate selectivity is encoded—what degrons and recognition features distinguish its many membrane substrates and how lipid, nucleotide, and partner inputs converge on a single processing decision—remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified substrate-recognition code defined","No structure of the full membrane-embedded SPY-assembled enzyme","Quantitative integration of PE, ATP, acetylation, and partner regulation not achieved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,14,19]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[1,7,14]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[11,18]}],"localization":[],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[1,2,19]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,7,14]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[6,14]}],"complexes":["SPY complex (SLP2-PARL-YME1L)"],"partners":["SLP2","PARL","ROMO1","KIF1BΒ","SIRT3","GCN5L1","BCL2L13"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96TA2","full_name":"ATP-dependent zinc metalloprotease YME1L1","aliases":["ATP-dependent metalloprotease FtsH1","Meg-4","Presenilin-associated metalloprotease","PAMP","YME1-like protein 1"],"length_aa":773,"mass_kda":86.5,"function":"ATP-dependent metalloprotease that catalyzes the degradation of folded and unfolded proteins with a suitable degron sequence in the mitochondrial intermembrane region (PubMed:24315374, PubMed:26923599, PubMed:27786171, PubMed:31695197, PubMed:33237841, PubMed:36206740). Plays an important role in regulating mitochondrial morphology and function by cleaving OPA1 at position S2, giving rise to a form of OPA1 that promotes maintenance of normal mitochondrial structure and mitochondrial protein metabolism (PubMed:18076378, PubMed:26923599, PubMed:27495975, PubMed:33237841). Ensures cell proliferation, maintains normal cristae morphology and complex I respiration activity, promotes antiapoptotic activity and protects mitochondria from the accumulation of oxidatively damaged membrane proteins (PubMed:22262461). Required to control the accumulation of nonassembled respiratory chain subunits (NDUFB6, OX4 and ND1) (PubMed:22262461). Involved in the mitochondrial adaptation in response to various signals, such as stress or developmental cues, by mediating degradation of mitochondrial proteins to rewire the mitochondrial proteome (PubMed:31695197). Catalyzes degradation of mitochondrial proteins, such as translocases, lipid transfer proteins and metabolic enzymes in response to nutrient starvation in order to limit mitochondrial biogenesis: mechanistically, YME1L is activated by decreased phosphatidylethanolamine levels caused by LPIN1 activity in response to mTORC1 inhibition (PubMed:31695197). Acts as a regulator of adult neural stem cell self-renewal by promoting mitochondrial proteome rewiring, preserving neural stem and progenitor cells self-renewal (By similarity). Required for normal, constitutive degradation of PRELID1 (PubMed:27495975). Catalyzes the degradation of OMA1 in response to membrane depolarization (PubMed:26923599). Mediates degradation of TIMM17A downstream of the integrated stress response (ISR) (PubMed:24315374). Catalyzes degradation of MICU1 when MICU1 is not assembled via an interchain disulfide (PubMed:36206740)","subcellular_location":"Mitochondrion inner membrane; Mitochondrion","url":"https://www.uniprot.org/uniprotkb/Q96TA2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/YME1L1","classification":"Not Classified","n_dependent_lines":345,"n_total_lines":1208,"dependency_fraction":0.2855960264900662},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/YME1L1","total_profiled":1310},"omim":[{"mim_id":"620399","title":"AARF DOMAIN-CONTAINING KINASE 1; ADCK1","url":"https://www.omim.org/entry/620399"},{"mim_id":"618894","title":"REACTIVE OXYGEN SPECIES MODULATOR 1; ROMO1","url":"https://www.omim.org/entry/618894"},{"mim_id":"617469","title":"AFG1-LIKE ATPase; AFG1L","url":"https://www.omim.org/entry/617469"},{"mim_id":"617302","title":"OPTIC ATROPHY 11; OPA11","url":"https://www.omim.org/entry/617302"},{"mim_id":"617267","title":"MATRIX AAA PEPTIDASE-INTERACTING PROTEIN 1; MAIP1","url":"https://www.omim.org/entry/617267"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Mitochondria","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in 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Loss of membrane potential destabilizes OPA1 long isoforms and enhances cleavage at S1 (but not S2), while S2 cleavage is specifically regulated by Yme1L.\",\n      \"method\": \"Cellular reconstitution in OPA1-null cells; shRNA knockdown of Yme1L; analysis of OPA1 isoform patterns by western blot\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean loss-of-function in defined null background, replicated across multiple labs subsequently\",\n      \"pmids\": [\"17709429\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Human YME1L is an integral inner mitochondrial membrane protein that exposes its carboxy-terminus to the intermembrane space and exists in large complexes of 600–1100 kDa. Its proteolytic activity is required for degrading non-assembled respiratory chain subunits (Ndufb6, ND1, Cox4), maintaining cristae morphology, supporting cell proliferation, and conferring apoptotic resistance.\",\n      \"method\": \"Stable shRNA knockdown in HEK293 cells; rescue with wild-type vs. proteolytically inactive YME1L mutant; electron microscopy; western blot; respiration assay\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO/rescue with catalytic mutant and multiple orthogonal readouts in single lab\",\n      \"pmids\": [\"22262461\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"YME1L performs constitutive cleavage of OPA1, and together with OMA1 generates both long and short OPA1 forms that maintain mitochondrial fusion. Short OPA1 forms produced by OMA1/YME1L processing promote mitochondrial fission and partially co-localize with ER-mitochondria contact sites and the fission machinery. Long OPA1 forms alone are sufficient to mediate fusion in the absence of both YME1L and OMA1.\",\n      \"method\": \"Genetic deletion of Yme1l, Oma1, or both; mitochondrial morphology imaging; epistasis analysis; co-localization of GTPase-inactive short OPA1 with fission machinery\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — double KO epistasis, replicated and extended by multiple subsequent labs\",\n      \"pmids\": [\"24616225\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Endogenous Yme1L localizes to punctate structures on mitochondria. Loss of Yme1L causes mitochondrial fragmentation through increased Drp1 recruitment (via elevated MiD49/Mff), not via OPA1 S1/S2 processing; shYme1L stabilizes L-OPA1 and exogenous OPA1/L-OPA1 further promotes fragmentation. SLP-2 interacts with Yme1L. Loss of Drp1 or Mff rescues shYme1L-induced fragmentation.\",\n      \"method\": \"shRNA knockdown in MEF cells; live-cell mitochondrial dynamics imaging; co-immunoprecipitation of SLP-2 with Yme1L; epistasis with Drp1/Mff KO\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — single lab, multiple orthogonal methods including live imaging and epistasis\",\n      \"pmids\": [\"24176854\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SLP2 anchors a large protease complex (SPY complex) at the mitochondrial inner membrane comprising PARL and YME1L. Association with SLP2 regulates PARL-mediated processing of PINK1 and PGAM5, and SLP2 inhibits OMA1-mediated OPA1 cleavage, thereby enabling stress-induced mitochondrial hyperfusion. SLP2 restricts OMA1 activity by direct binding.\",\n      \"method\": \"Co-immunoprecipitation; blue-native PAGE complex analysis; genetic deletion/knockdown of SLP2; processing assays for PINK1, PGAM5, OPA1; mitochondrial morphology imaging under starvation stress\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, multiple substrate processing assays, genetic KO with functional rescue in single thorough study\",\n      \"pmids\": [\"27737933\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"A homozygous missense mutation in the mitochondrial pre-sequence of YME1L1 inhibits its cleavage by the mitochondrial processing peptidase (MPP), leading to rapid degradation of the YME1L1 precursor protein. This abolishes YME1L1 function, causes abnormal OPA1 processing, mitochondrial network fragmentation, and a proliferation defect in patient-derived cells.\",\n      \"method\": \"Patient fibroblast studies; western blot for precursor vs. mature YME1L1; OPA1 isoform analysis; mitochondrial morphology imaging; genetic complementation\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — human disease variant functionally validated with multiple orthogonal assays in patient-derived cells\",\n      \"pmids\": [\"27495975\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ROMO1 is a constituent of the human TIM23 presequence translocase that is specifically required for import of YME1L into the inner mitochondrial membrane. Loss of ROMO1 causes selective loss of YME1L (but not general presequence import), leading to aberrant OPA1 processing and inner membrane structural defects. This selective requirement is linked to the unusually long and charge-distributed targeting sequence of YME1L.\",\n      \"method\": \"Mass spectrometry identification of TIM23 complex components; ROMO1 knockout cell line; quantitative proteomics; protein import assays; OPA1 processing assay; inner membrane morphology by EM\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — MS-defined complex, KO cell line, import assay with defined mechanistic link to YME1L targeting sequence\",\n      \"pmids\": [\"30598479\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"YME1L rewires the mitochondrial proteome in response to hypoxia or nutrient starvation via a lipid signalling cascade. Inhibition of mTORC1 activates LIPIN1 phosphatidic acid phosphatase, which decreases mitochondrial phosphatidylethanolamine levels and promotes YME1L-mediated proteolysis of mitochondrial protein translocases, lipid transfer proteins, and metabolic enzymes, acutely limiting mitochondrial biogenesis while supporting cell growth.\",\n      \"method\": \"Quantitative mitochondrial proteomics under hypoxia/starvation; mTORC1 inhibition; LIPIN1 genetic manipulation; lipid mass spectrometry for PE levels; YME1L KO; xenograft tumor models\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (proteomics, lipidomics, genetics, in vivo), rigorous mechanistic pathway dissection\",\n      \"pmids\": [\"31695197\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"YME1L-deficient mice lacking YME1L in the nervous system develop ocular dysfunction and selective degeneration of spinal cord proprioceptive axons. Deletion of Oma1 in Yme1l-null mice restores tubular mitochondria but worsens axonal degeneration, establishing that impaired mitochondrial proteostasis (not mitochondrial fragmentation per se) causes the neurological defects.\",\n      \"method\": \"Conditional nervous-system-specific Yme1l KO mice; double Yme1l/Oma1 KO epistasis; histological and behavioral analysis; mitochondrial morphology imaging\",\n      \"journal\": \"EMBO molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo conditional KO with double-KO epistasis dissecting fragmentation from proteostasis roles\",\n      \"pmids\": [\"30389680\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"KIF1Bβ physically interacts with YME1L1 through its death-inducing region and stimulates YME1L1 protease activity to cleave long OPA1 forms, causing mitochondrial fragmentation and apoptosis. Both KIF1Bβ and YME1L1 are upregulated upon NGF withdrawal in PC12 cells, and knockdown of either protein inhibits NGF-depletion-induced apoptosis.\",\n      \"method\": \"Co-immunoprecipitation of KIF1Bβ with YME1L1; domain-mapping with deletion constructs; OPA1 cleavage assay; siRNA knockdown of each protein; NGF-withdrawal apoptosis model\",\n      \"journal\": \"Molecular carcinogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single lab, Co-IP plus functional assay but no in vitro reconstitution of stimulated protease activity\",\n      \"pmids\": [\"30859632\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Loss of Yme1L in C2C12 myotubes activates AMPK and FoxO3a and increases expression of MuRF1 and myostatin, contributing to muscle atrophy. Yme1L depletion causes accumulation of short OPA1 forms and mitochondrial fragmentation, and this effect is specific to Yme1L (not LonP1).\",\n      \"method\": \"shRNA knockdown of Yme1L in C2C12 myotubes; hindlimb-immobilized mouse model; western blot for OPA1 isoforms, AMPK, FoxO3a, MuRF1, myostatin; mitochondrial morphology\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, defined cellular phenotype with pathway markers but no reconstitution or epistasis for pathway placement\",\n      \"pmids\": [\"31725201\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ATP binding stabilizes the hexameric structure of the YME1L catalytic domain and protects it from urea-induced unfolding and loss of active hexamers, as measured by fluorescence unfolding and stopped-flow nucleotide-binding assays.\",\n      \"method\": \"Protein unfolding fluorescence assay with urea; stopped-flow fluorescence for nucleotide binding and unfoldase activity; multiple fluorophore systems\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro biochemical assay on purified protein but single lab, single study\",\n      \"pmids\": [\"32340357\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"YME1L controls the abundance of numerous mitochondrial substrates in quiescent neural stem and progenitor cells (NSPCs). Conditional Yme1l deletion activates a differentiation program with broad metabolic changes, irreversibly shifting NSPCs away from a fatty-acid-oxidation-dependent state and causing premature differentiation and NSPC pool depletion in vivo.\",\n      \"method\": \"Conditional Yme1l KO in adult NSPCs in vivo; quantitative mitochondrial proteomics; metabolic profiling; fate-mapping and self-renewal assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo conditional KO with proteomics and metabolic phenotyping, multiple orthogonal readouts\",\n      \"pmids\": [\"35172139\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Sirt3 deacetylates YME1L1, and this deacetylation promotes OPA1-mediated mitochondrial fusion. Loss of Sirt3 increases YME1L1 acetylation and impairs fusion; Sirt3 overexpression rescues LPS-induced mitochondrial damage and apoptosis in renal tubular epithelial cells via the YME1L1-OPA1 axis.\",\n      \"method\": \"Sirt3 KO mice + LPS model; Sirt3 overexpression in HK-2 cells; co-immunoprecipitation; deacetylation assay; OPA1 processing analysis; mitochondrial morphology by immunofluorescence and electron microscopy\",\n      \"journal\": \"Cell proliferation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse plus cellular overexpression, Co-IP for interaction, but acetylation site not mapped by mutagenesis\",\n      \"pmids\": [\"36433732\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Plugging the TOM complex in mammalian cells induces YME1L1-dependent degradation of TIM23 channel components TIMM17A and TIMM23. Unoccupied TIM23 complexes appear to expose a C-terminal degron on TIMM17A that is recognized by YME1L1 for proteolysis. Loss of YME1L1 exacerbates the growth defect caused by TOM channel plugging.\",\n      \"method\": \"DHFR-MIC60 import-blocking system stabilized by methotrexate; YME1L1 KO cell lines; western blot for TIMM17A/TIMM23 levels; cell growth assays\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined genetic system with KO, multiple substrates identified, functional consequence measured\",\n      \"pmids\": [\"39774271\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"YME1L1 directly degrades SLC25A38, a short-lived mitochondrial glycine transporter (half-life ~4 h). Pharmacological inhibition or genetic depletion of YME1L1 stabilizes SLC25A38. Depolarization of mitochondrial membrane potential by CCCP prevents SLC25A38 degradation, linking its turnover to inner membrane integrity.\",\n      \"method\": \"Protein half-life analysis; pharmacological inhibition of proteolytic systems; YME1L1 genetic depletion; CCCP depolarization experiment; western blot for SLC25A38 stability\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic and pharmacological evidence in single preprint, no in vitro reconstitution\",\n      \"pmids\": [\"38979268\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"YME1L interacts with BCL2L13 (a mitophagy receptor) and promotes its phosphorylation, thereby enhancing mitophagy in renal tubular epithelial cells. LC-MS/MS identified BCL2L13 as a YME1L-interacting protein.\",\n      \"method\": \"LC-MS/MS interactome analysis; co-immunoprecipitation; phosphorylation assay; in vivo AAV-mediated YME1L overexpression; mitophagy flux assays\",\n      \"journal\": \"Biological research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, MS-identified interaction with limited mechanistic follow-up on phosphorylation\",\n      \"pmids\": [\"38494498\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A novel homozygous YME1L1 variant (p.Leu667Val) causes defective proteolytic processing of OPA1 and PRELID1 (PRELI domain containing 1), enhanced mitochondrial fission, attenuated Krebs cycle enzyme activities, and reduced mitochondrial respiration in patient fibroblasts, classifying YME1L1 deficiency as a form of secondary 3-methylglutaconic aciduria.\",\n      \"method\": \"Patient fibroblast functional studies; OPA1 and PRELID1 processing assays; mitochondrial morphology imaging; Krebs cycle enzyme activity assays; mitochondrial respiration measurement\",\n      \"journal\": \"Journal of inherited metabolic disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal functional assays in patient-derived cells, single lab\",\n      \"pmids\": [\"40255048\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Nucleotide (ATP) binding reduces backbone flexibility and modulates side-chain dynamics of the AAA+ domain of YME1L, while Zn²⁺ binding stabilizes the protease domain. Long-range allostery between the AAA+ and protease domains is mediated by a critical salt bridge at the inter-domain interface, and disruption of this salt bridge impairs ATP-dependent substrate degradation.\",\n      \"method\": \"HDX-MS; NMR spectroscopy; site-directed mutagenesis of salt bridge residue; in vitro substrate degradation assay with hexameric soluble YME1L construct\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — Tier 1 methods (HDX-MS, NMR, mutagenesis + in vitro assay) in single preprint, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.01.30.635686\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"GCN5L1 physically associates with YME1L in the mitochondrial intermembrane space and facilitates YME1L-mediated degradation of the MICOS component MIC13, thereby promoting cristae disassembly during obesity. A high-fat diet triggers GCN5L1 accumulation in the intermembrane space, activating this pathway.\",\n      \"method\": \"Protein interactome analysis (GCN5L1 KO mice); co-immunoprecipitation; MIC13 degradation assay; cristae morphology by EM; metabolic phenotyping of adipose-specific KO mice\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — interactome plus genetic KO with functional substrate (MIC13) degradation assay, single lab\",\n      \"pmids\": [\"40338741\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"YME1L1 is an ATP-dependent i-AAA metalloprotease anchored in the mitochondrial inner membrane with its catalytic domain facing the intermembrane space, where it constitutively cleaves OPA1 at site S2 (together with OMA1 at S1) to generate both long and short OPA1 isoforms that balance mitochondrial fusion and fission; it also performs quality-control proteolysis of non-assembled respiratory chain subunits, mitochondrial translocases (TIMM17A, TIMM23), lipid transfer proteins, metabolic enzymes, and the glycine transporter SLC25A38, with its proteolytic activity allosterically regulated by ATP binding and inter-domain salt-bridge communication, assembled within the SLP2-PARL-YME1L (SPY) scaffold complex, imported into the inner membrane via a ROMO1-dependent TIM23 pathway, and subject to activity modulation by Sirt3-mediated deacetylation and by mTORC1-LIPIN1-driven changes in phosphatidylethanolamine levels.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"YME1L1 is an ATP-dependent inner mitochondrial membrane protease that governs mitochondrial morphology and proteostasis by exposing a catalytic domain to the intermembrane space and assembling into large (600–1100 kDa) complexes [#0, #1]. It constitutively cleaves OPA1 at site S2 and, together with OMA1, generates the balance of long and short OPA1 isoforms that set the equilibrium between mitochondrial fusion and fission [#0, #2]. Beyond this central dynamics role, YME1L1 performs quality-control proteolysis of a broad substrate set including non-assembled respiratory chain subunits, where this activity maintains cristae morphology, respiration, proliferation, and apoptotic resistance [#1], the TIM23 translocase channel components TIMM17A and TIMM23 when their import channel is unoccupied [#14], lipid transfer proteins and metabolic enzymes [#7], and the MICOS subunit MIC13 [#19]. This proteolysis is mobilized as an adaptive program: mTORC1 inhibition activates LIPIN1, lowering mitochondrial phosphatidylethanolamine and triggering YME1L1-mediated remodeling of the mitochondrial proteome to limit biogenesis while supporting growth under hypoxia or starvation [#7]. YME1L1 is anchored within the SLP2–PARL–YME1L (SPY) scaffold at the inner membrane [#3, #4] and is selectively imported through a ROMO1-dependent TIM23 pathway [#6]. In vivo, loss of YME1L1 causes neurodegeneration driven by impaired proteostasis rather than fragmentation per se [#8] and depletes neural stem/progenitor pools by forcing premature differentiation [#12]. Human homozygous YME1L1 mutations that abolish or impair function cause defective OPA1 processing, mitochondrial fragmentation, and a mitochondriopathy classified as a form of secondary 3-methylglutaconic aciduria [#5, #17].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Establishing which protease produces a specific OPA1 isoform answered how a single dynamin-related GTPase is post-translationally diversified to control fusion; YME1L was identified as the S2-cleaving enzyme.\",\n      \"evidence\": \"shRNA knockdown of Yme1L and OPA1 isoform analysis in OPA1-null reconstituted cells\",\n      \"pmids\": [\"17709429\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve full substrate spectrum beyond OPA1\", \"Did not establish the regulatory inputs controlling S2 cleavage\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defining YME1L topology and catalytic requirement showed it is a bona fide proteolytic quality-control enzyme rather than a passive scaffold, linking its activity to respiratory chain integrity and cell survival.\",\n      \"evidence\": \"shRNA knockdown with wild-type vs. catalytically dead rescue, EM, respiration assays in HEK293\",\n      \"pmids\": [\"22262461\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrate recognition mechanism not defined\", \"Composition of the 600–1100 kDa complexes not resolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Double-knockout epistasis with OMA1 clarified how two proteases jointly set the long/short OPA1 ratio and demonstrated that long OPA1 forms suffice for fusion.\",\n      \"evidence\": \"Yme1l/Oma1 single and double genetic deletion, morphology imaging, co-localization of short OPA1 with fission machinery\",\n      \"pmids\": [\"24616225\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish how cleavage choice between OMA1 and YME1L is partitioned\", \"Stoichiometry of short-OPA1 action at fission sites unresolved\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Characterizing the SLP-2 interaction and the Drp1/Mff-dependent fragmentation phenotype showed YME1L influences fission through the recruitment machinery, not only via OPA1 processing.\",\n      \"evidence\": \"shRNA knockdown in MEFs, live imaging, Co-IP of SLP-2, epistasis with Drp1/Mff knockout\",\n      \"pmids\": [\"24176854\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Mechanistic link between YME1L loss and elevated MiD49/Mff not defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identifying the SPY complex placed YME1L within a defined inner-membrane proteolytic scaffold alongside SLP2 and PARL, contextualizing how multiple processing reactions are spatially organized.\",\n      \"evidence\": \"Reciprocal Co-IP, blue-native PAGE, SLP2 deletion with PINK1/PGAM5/OPA1 processing assays\",\n      \"pmids\": [\"27737933\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct biochemical architecture of the SPY complex not solved\", \"How SLP2 binding modulates YME1L catalysis specifically not dissected\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"A patient pre-sequence mutation that blocks MPP cleavage established YME1L1 as a human disease gene and demonstrated that loss of mature protein recapitulates OPA1 and morphology defects.\",\n      \"evidence\": \"Patient fibroblast studies, precursor/mature western blot, OPA1 analysis, genetic complementation\",\n      \"pmids\": [\"27495975\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full clinical-molecular spectrum not defined from a single family\", \"Tissue-specific vulnerability not explained\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Discovering the ROMO1-dependent TIM23 import route explained how YME1L is selectively delivered to the inner membrane and why its unusual targeting sequence creates a specific import dependency.\",\n      \"evidence\": \"MS identification of TIM23 components, ROMO1 KO, import assays, quantitative proteomics, EM\",\n      \"pmids\": [\"30598479\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Biochemical basis of ROMO1 recognition of the YME1L pre-sequence not solved\", \"Whether other inner-membrane proteins share this route not fully mapped\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Linking mTORC1–LIPIN1–phosphatidylethanolamine signaling to YME1L proteolysis revealed how the protease acts as an adaptive sensor that remodels the mitochondrial proteome in response to nutrient and oxygen stress.\",\n      \"evidence\": \"Quantitative proteomics and lipidomics under hypoxia/starvation, mTORC1 inhibition, LIPIN1 manipulation, YME1L KO, xenografts\",\n      \"pmids\": [\"31695197\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How lowered PE mechanistically activates YME1L not resolved at the molecular level\", \"Substrate selectivity rules under remodeling not defined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Nervous-system conditional knockout with Oma1 epistasis separated YME1L's proteostasis function from morphology, showing that proteostatic failure—not fragmentation—drives neurodegeneration.\",\n      \"evidence\": \"Conditional Yme1l KO mice, Yme1l/Oma1 double KO, histology, behavior, morphology imaging\",\n      \"pmids\": [\"30389680\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific substrate(s) responsible for axonal degeneration not identified\", \"Cell-type basis of proprioceptive selectivity unexplained\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identifying KIF1Bβ as a stimulatory binding partner provided a mechanism for inducible YME1L activation during apoptotic signaling.\",\n      \"evidence\": \"Co-IP, domain mapping, OPA1 cleavage assay, siRNA, NGF-withdrawal apoptosis model in PC12\",\n      \"pmids\": [\"30859632\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vitro reconstitution of stimulated protease activity\", \"Single lab\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Muscle-cell depletion connected YME1L loss to AMPK/FoxO3a-driven atrophy programs, extending its physiological reach to muscle homeostasis.\",\n      \"evidence\": \"shRNA in C2C12 myotubes, immobilization mouse model, western blots for OPA1/AMPK/FoxO3a/MuRF1/myostatin\",\n      \"pmids\": [\"31725201\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No epistasis to place YME1L upstream of AMPK\", \"Direct substrate driving atrophy not identified\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Biochemical study of ATP binding showed nucleotide stabilizes the hexameric catalytic assembly, beginning the mechanistic dissection of allosteric control.\",\n      \"evidence\": \"Urea unfolding fluorescence and stopped-flow nucleotide-binding assays on purified protein\",\n      \"pmids\": [\"32340357\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single in vitro study\", \"Did not link nucleotide state to substrate processing on membranes\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Conditional knockout in neural stem/progenitor cells demonstrated YME1L sets a metabolic state required for quiescence, with its loss forcing premature differentiation and pool depletion.\",\n      \"evidence\": \"In vivo conditional Yme1l KO, mitochondrial proteomics, metabolic profiling, fate-mapping\",\n      \"pmids\": [\"35172139\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Key substrate controlling the fatty-acid-oxidation state not pinpointed\", \"Reversibility window not defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identifying Sirt3-mediated deacetylation of YME1L1 established a post-translational regulatory layer coupling NAD+-dependent signaling to mitochondrial fusion.\",\n      \"evidence\": \"Sirt3 KO mice + LPS, HK-2 overexpression, Co-IP, deacetylation and OPA1 processing assays\",\n      \"pmids\": [\"36433732\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Acetylation site not mapped by mutagenesis\", \"Direct effect of acetylation on catalytic activity not measured biochemically\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"An import-blocking system revealed YME1L1 degrades unoccupied TIM23 channel subunits via an exposed degron, defining a surveillance role over the translocase itself.\",\n      \"evidence\": \"DHFR-MIC60 import-block, YME1L1 KO cells, western blots for TIMM17A/TIMM23, growth assays\",\n      \"pmids\": [\"39774271\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Degron sequence not precisely defined\", \"Whether degradation is direct (not via cofactor) not biochemically reconstituted\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identifying SLC25A38 as a short-lived YME1L1 substrate linked the protease to control of a mitochondrial glycine transporter and tied turnover to membrane potential.\",\n      \"evidence\": \"Half-life analysis, pharmacological/genetic YME1L1 depletion, CCCP depolarization, western blot (preprint)\",\n      \"pmids\": [\"38979268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vitro reconstitution of direct cleavage\", \"Preprint, not peer-reviewed\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A reported interaction with the mitophagy receptor BCL2L13 raised the possibility that YME1L participates in mitophagy regulation.\",\n      \"evidence\": \"LC-MS/MS interactome, Co-IP, phosphorylation assay, AAV overexpression, mitophagy flux assays\",\n      \"pmids\": [\"38494498\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single lab with limited mechanistic follow-up on the phosphorylation step\", \"Whether the effect requires YME1L catalytic activity not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"A second human homozygous variant (p.Leu667Val) expanded the disease phenotype, linking defective OPA1 and PRELID1 processing to impaired Krebs cycle activity and classifying the deficiency within 3-methylglutaconic aciduria.\",\n      \"evidence\": \"Patient fibroblast OPA1/PRELID1 processing, morphology imaging, Krebs cycle enzyme and respiration assays\",\n      \"pmids\": [\"40255048\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Genotype-phenotype correlation across patients not established\", \"Mechanism linking PRELID1 mis-processing to metabolic defect not dissected\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Structural-dynamics analysis defined an inter-domain salt bridge mediating AAA+-to-protease allostery, explaining how ATP and Zn2+ binding are communicated to control substrate degradation.\",\n      \"evidence\": \"HDX-MS, NMR, salt-bridge mutagenesis, in vitro degradation assay with soluble hexameric construct (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.01.30.635686\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"Full-length membrane-embedded enzyme not structurally resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identifying GCN5L1 as an intermembrane-space partner that promotes YME1L-mediated MIC13 degradation connected the protease to diet-induced cristae remodeling.\",\n      \"evidence\": \"GCN5L1 KO interactome, Co-IP, MIC13 degradation assay, EM, adipose-specific KO metabolic phenotyping\",\n      \"pmids\": [\"40338741\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Direct vs. cofactor-assisted MIC13 cleavage not reconstituted\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How YME1L's substrate selectivity is encoded—what degrons and recognition features distinguish its many membrane substrates and how lipid, nucleotide, and partner inputs converge on a single processing decision—remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified substrate-recognition code defined\", \"No structure of the full membrane-embedded SPY-assembled enzyme\", \"Quantitative integration of PE, ATP, acetylation, and partner regulation not achieved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 14, 19]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [1, 7, 14]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [11, 18]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005743\", \"supporting_discovery_ids\": [0, 1, 6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [1, 2, 19]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 7, 14]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [6, 14]}\n    ],\n    \"complexes\": [\"SPY complex (SLP2-PARL-YME1L)\"],\n    \"partners\": [\"SLP2\", \"PARL\", \"ROMO1\", \"KIF1B\\u03b2\", \"SIRT3\", \"GCN5L1\", \"BCL2L13\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}