{"gene":"AARS1","run_date":"2026-06-09T22:02:35","timeline":{"discoveries":[{"year":2024,"finding":"AARS1 functions as a lactate sensor that binds lactate with micromolar affinity and catalyzes ATP-dependent formation of lactyl-AMP, which is then transferred to lysine acceptor residues on target proteins, establishing AARS1 as a bona fide lactyltransferase enzyme.","method":"In vitro biochemical assay (ATP-dependent lactylation), binding assays, proteomics","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro enzymatic reconstitution of lactylation activity demonstrated in two independent labs (PMID:38653238 and PMID:39322678) with multiple orthogonal methods","pmids":["38653238","39322678","38512451"],"is_preprint":false},{"year":2024,"finding":"AARS1 lactylates p53 at lysine 120 and lysine 139 in the DNA-binding domain, hindering p53 liquid-liquid phase separation, DNA binding, and transcriptional activation, as demonstrated using constitutively lactylated p53 variants.","method":"Proteomics, generation of constitutively lactylated lysine variants, in vitro DNA binding assays, phase separation assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro functional validation with engineered p53 variants plus proteomics, single lab but multiple orthogonal methods","pmids":["38653238"],"is_preprint":false},{"year":2024,"finding":"AARS2 (the mitochondrial paralog) associates with cGAS and mediates its lactylation; lactylation at a specific N-terminal site abolishes cGAS liquid-like phase separation and DNA sensing in vitro and in vivo, as confirmed by a genetic code expansion lactyl-lysine incorporation system and knock-in mice.","method":"Co-immunoprecipitation, genetic code expansion (orthogonal system for lactyl-lysine incorporation), knock-in mouse models, in vitro phase separation assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstitution of lactylation activity, genetic knock-in validation in mice, multiple orthogonal methods in a single rigorous study; note this finding is primarily about AARS2 but the paper establishes the shared lactylation mechanism for both AARS1 and AARS2","pmids":["39322678"],"is_preprint":false},{"year":2024,"finding":"AARS1 senses intracellular lactate and translocates into the nucleus, where it lactylates and activates the YAP-TEAD complex; AARS1 itself is a Hippo target gene forming a positive-feedback loop with YAP-TEAD to promote gastric cancer cell proliferation.","method":"In vitro lactyltransferase assay, nuclear translocation imaging, reporter assays, loss-of-function studies","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — direct in vitro lactyltransferase activity demonstrated, nuclear translocation documented, feedback loop established by multiple methods in a single lab","pmids":["38512451"],"is_preprint":false},{"year":2011,"finding":"The CMT2N disease-associated p.Arg329His mutation in AARS1 severely reduces aminoacylation (tRNA charging) enzyme activity, as demonstrated by aminoacylation assays and yeast viability complementation assays.","method":"In vitro aminoacylation assay, yeast complementation assay","journal":"Human mutation","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct in vitro enzymatic assay plus yeast functional complementation, replicated in multiple families and independently confirmed","pmids":["22009580"],"is_preprint":false},{"year":2009,"finding":"AlaRS (AARS1) has an inherent structural dilemma in amino acid recognition: an acidic residue required to pin down the alpha-amino group of alanine serendipitously interacts with the serine OH, explaining why serine is misactivated. Nine crystal structures and kinetic/mutational analysis provided the mechanistic basis.","method":"X-ray crystallography (9 structures), kinetic assays, site-directed mutagenesis","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple crystal structures combined with kinetic and mutational analysis in one rigorous study","pmids":["20010690"],"is_preprint":false},{"year":2021,"finding":"AARS1 variants causing trichothiodystrophy result in instability of the alanyl-tRNA synthetase protein and a reduced rate of tRNA charging (aminoacylation), as demonstrated by functional studies in patient-derived skin fibroblasts.","method":"tRNA charging activity assay in patient fibroblasts, protein stability assessment","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct enzymatic activity measurement in patient cells, two orthogonal readouts (protein stability and tRNA charging), single lab","pmids":["33909043"],"is_preprint":false},{"year":2021,"finding":"CMT2N-associated mutations in the aminoacylation domain of AlaRS (including R329H) induce structural loosening of the aminoacylation domain, enabling aberrant gain-of-function binding to neuropilin 1 (Nrp1); this interaction was confirmed in patient samples and the b1b2 domains of Nrp1 are responsible. Notably, R329H is aminoacylation-normal as a purified protein in vitro.","method":"X-ray crystallography, small-angle X-ray scattering, hydrogen-deuterium exchange (HDX), switchSENSE hydrodynamic diameter, protease digestion, Co-immunoprecipitation in patient cells","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple biophysical and structural methods plus patient-sample validation confirming AlaRS-Nrp1 interaction, single rigorous study with extensive orthogonal evidence","pmids":["33753480"],"is_preprint":false},{"year":2016,"finding":"Crystal structures of human C-Ala (the C-terminal domain of AlaRS) revealed that sequence divergence from prokaryotic C-Ala reshaped the domain architecture, forming a dimer interface with a DNA-binding groove; direct DNA binding by human C-Ala (but not bacterial C-Ala) was demonstrated, indicating a repurposing of this domain in higher organisms.","method":"X-ray crystallography (two crystal forms of human C-Ala), small-angle X-ray scattering, in vitro DNA binding assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures combined with functional DNA binding assay in a single rigorous study","pmids":["27911835"],"is_preprint":false},{"year":2017,"finding":"D-aminoacyl-tRNA deacylase (DTD) edits mischarged Gly-tRNAAla species (generated by AARS1 mischarging) four orders of magnitude more efficiently than AARS1's own editing activity; DTD knockout in an AlaRS editing-defective background causes pronounced toxicity in E. coli, establishing DTD as a secondary cellular checkpoint for glycine mischarging by AlaRS.","method":"In vitro editing/deacylation kinetic assays, genetic epistasis (DTD knockout in AlaRS editing-defective background), in vivo toxicity rescue by alanine supplementation","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro kinetic reconstitution plus genetic epistasis with multiple controls","pmids":["28362257"],"is_preprint":false},{"year":2018,"finding":"CMT2N-associated AARS1 mutations include both loss-of-function (hypomorphic: p.Ser627Leu, p.Arg326Trp) and gain-of-function (hypermorphic: p.Glu337Lys) alleles; yeast complementation demonstrated the functional class of each, and aminoacylation assays confirmed p.Glu337Lys increases tRNA charging velocity. All three caused neural abnormalities in zebrafish.","method":"Yeast complementation assay, in vitro aminoacylation assay, zebrafish expression model","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct enzymatic assay plus yeast complementation plus zebrafish model, multiple orthogonal methods in a single lab","pmids":["30124830"],"is_preprint":false},{"year":2018,"finding":"The CMT2N-associated N71Y mutation of AARS1 causes mislocalization of the protein to lysosomes (instead of cytoplasm) in COS-7 cells, and expression of this mutant in N1E-115 neuronal cells inhibits neurite process growth; this inhibition is reversed by pretreatment with valproic acid.","method":"Immunofluorescence localization, neuronal process growth assay, pharmacological rescue","journal":"Neuroscience research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization experiment and functional neuronal phenotype, two cell line models, single lab","pmids":["30261202"],"is_preprint":false},{"year":2015,"finding":"A novel AARS1 p.Gly102Arg mutation fails to complement yeast lacking AARS function, demonstrating the mutation is damaging to tRNA synthetase activity; affected individuals present with myeloneuropathy.","method":"Yeast complementation assay","journal":"Neurology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — yeast complementation is a functional assay but single method, single lab","pmids":["25904691"],"is_preprint":false},{"year":2020,"finding":"AARS1 deficiency variants (p.Leu298Gln; p.Arg751Gly) cause decreased aminoacylation (tRNA charging) enzymatic activity in patient-derived fibroblasts, associated with recurrent acute liver failure.","method":"Enzymatic activity assay in patient fibroblasts","journal":"Molecular genetics and metabolism reports","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct enzymatic activity measurement in patient cells, single lab, single method","pmids":["33294374"],"is_preprint":false},{"year":2025,"finding":"AARS1 lactylates BLM helicase at Lys24, improving BLM protein stability by inhibiting MIB1-mediated ubiquitination and increasing its interaction with DNA repair factors, thereby promoting DNA end resection and homologous recombination repair, which drives chemoresistance to anthracyclines.","method":"Co-immunoprecipitation, mass spectrometry, global lactylome profiling, Lys24 mutation (delactylation), ubiquitination assay","journal":"Signal transduction and targeted therapy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, mass spectrometry, mutation-based functional validation, single lab but multiple orthogonal methods","pmids":["40634292"],"is_preprint":false},{"year":2025,"finding":"AARS1 lactylates histone H3K18 and STAT1, and interacts with STAT1 to jointly regulate ELOVL5 transcription, inducing lipid peroxidation and ferroptosis in diabetic nephropathy; β-alanine inhibits AARS1-mediated lactylation and attenuates ferroptosis in model mice.","method":"Co-immunoprecipitation, transcriptomic and lipidomic analyses, AARS1 heterozygous mouse model, molecular biological assays","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for AARS1-STAT1 interaction, in vivo mouse model, multiple readouts; single lab","pmids":["40987895"],"is_preprint":false},{"year":2026,"finding":"AARS1 lactylates STAT1 at K193, inhibiting its binding to JAK2 and phosphorylation, thereby disrupting IFN-γ signaling and reducing downstream chemokine expression (CXCL9/10/11), facilitating tumor immune escape; a cell-penetrating peptide targeting K193 lactylation restored IFN-γ responsiveness.","method":"Co-immunoprecipitation, phosphorylation assays, loss-of-function studies, peptide inhibitor","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding/phosphorylation assays, mechanistic peptide rescue, single lab","pmids":["41832952"],"is_preprint":false},{"year":2025,"finding":"AARS1 directly lactylates Akt and the NF-κB subunit p65, enhancing their phosphorylation and activation, which impairs autophagy, promotes inflammation and tubular injury in diabetic kidney disease; kidney-specific Aars1 knockout or β-alanine treatment reduced these effects in mouse models.","method":"CUT and Tag, ChIP assays, luciferase reporter assays, CRISPR/Cas9 KO cells, kidney-specific knockout mice, streptozotocin and db/db diabetic models","journal":"Cellular & molecular biology letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct lactylation of substrates with in vivo KO validation, multiple methods, single lab","pmids":["42215867"],"is_preprint":false},{"year":2025,"finding":"A single-point mutation L219M in AlaRS (from Methylomonas sp.) eliminates serine misactivation; structural analysis revealed that flexibility of Val204 is key to blocking serine binding in the mutant. The same mutation also eliminates the enzyme's inherent lactyltransferase activity, linking the lactate-binding/activation pocket to the serine misactivation mechanism.","method":"X-ray crystallography (pre-activation state structure), in vitro aminoacylation kinetic assays, in vitro lactyltransferase assay, site-directed mutagenesis","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — crystal structure plus in vitro assays, bacterial ortholog, single lab","pmids":["40479712"],"is_preprint":false},{"year":2026,"finding":"AARS1 catalyzes lactylation of ATRIP at K127 in neuronal processes during sepsis, triggering ATRIP-ATR complex formation and pathway activation independent of DNA damage, causing excessive autophagy, synaptic dysfunction and neuronal process injury; L-alanine competitively inhibits lactate binding to AARS1 and suppresses this signaling.","method":"In vivo CLP sepsis mouse model, AARS1 knockdown, ATR inhibitor, lactylation site mapping, behavioral assays","journal":"Brain, behavior, and immunity","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo mouse model with pharmacological and genetic inhibition, site-specific lactylation, single lab","pmids":["41713664"],"is_preprint":false},{"year":2025,"finding":"AARS1 lactylates Osterix (Osx) transcription factor, increasing its binding to target gene promoters and promoting interaction with WDR5, which facilitates H3K4 tri-methylation on downstream target genes, enhancing osteoblast differentiation; silencing of AARS1 impaired alkaline phosphatase activity and mineralized nodule formation.","method":"Chromatin immunoprecipitation, Co-immunoprecipitation, loss-of-function knockdown, ALP activity assay, Alizarin Red staining","journal":"Acta histochemica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and Co-IP with functional osteoblast differentiation assays, single lab","pmids":["40505545"],"is_preprint":false},{"year":2026,"finding":"AARS1 mediates lactylation of AKR1B10 at K173, stabilizing AKR1B10 by blocking MIB1-mediated ubiquitin-proteasomal degradation; stabilized AKR1B10 interacts with LDHA, promotes LDHA Y10 phosphorylation and glycolytic lactate production, which drives H3K18 lactylation and transcriptional upregulation of LDHA, forming a self-reinforcing circuit driving lenvatinib resistance in HCC.","method":"Co-immunoprecipitation, mass spectrometry, ubiquitination assay, western blot, functional metabolic assays (Seahorse XF)","journal":"Clinical and translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, MS-based PTM mapping, ubiquitination assay, single lab","pmids":["41454479"],"is_preprint":false},{"year":2024,"finding":"Comprehensive humanized yeast model assessment of AARS1 recessive disease variants showed the majority cause variable loss-of-function effects; K81T AARS1 demonstrated both loss-of-function and dominant-negative effects, indicating certain AARS1 variants can cause both dominant and recessive phenotypes.","method":"Humanized yeast complementation assay (side-by-side comparison of all reported recessive missense variants)","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic yeast complementation with dominant-negative testing, preprint, single lab","pmids":["38979321"],"is_preprint":true},{"year":2025,"finding":"AARS1 promotes endometriosis by lactylating Snail1 to maintain its protein stability, enhancing epithelial-to-mesenchymal transition in endometriotic stromal cells.","method":"Co-immunoprecipitation, loss-of-function knockdown, cell proliferation/migration/invasion assays","journal":"Biology of reproduction","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP plus functional cellular assays, single lab, limited mechanistic detail in abstract","pmids":["40815826"],"is_preprint":false}],"current_model":"AARS1 is a bifunctional enzyme that (1) performs its canonical role as an alanyl-tRNA synthetase, charging tRNA with alanine via an ATP-dependent mechanism with a G3:U70 tRNA recognition element and an editing domain that proofreads serine and glycine mischarging, and (2) moonlights as an intracellular lactate sensor and lactyltransferase that binds lactate with micromolar affinity, catalyzes formation of lactyl-AMP, and transfers the lactyl moiety to lysine residues on diverse substrates including p53, YAP-TEAD, cGAS, BLM, STAT1, Akt, NF-κB/p65, and histone H3K18, thereby linking cellular lactate metabolism to epigenetic regulation, immune signaling, DNA repair, and oncogenesis; CMT2N-associated mutations in its aminoacylation domain induce structural loosening that enables aberrant gain-of-function binding to neuropilin 1 (Nrp1), while loss-of-function mutations reduce tRNA charging activity causing peripheral neuropathy or multi-system disease."},"narrative":{"mechanistic_narrative":"AARS1 is a bifunctional protein that couples canonical protein synthesis to lactate-driven signaling and epigenetic control [PMID:38653238, PMID:39322678, PMID:38512451]. In its housekeeping role it is an alanyl-tRNA synthetase whose active site has an inherent amino-acid recognition dilemma: an acidic residue that pins the alpha-amino group of alanine also engages the serine hydroxyl, accounting for serine misactivation, which is corrected by an editing function and backed up cellularly by the independent deacylase DTD that clears mischarged Gly-tRNA-Ala [PMID:20010690, PMID:28362257]. The C-terminal C-Ala domain has been structurally repurposed in humans to form a dimer interface with a DNA-binding groove [PMID:27911835]. Beyond aminoacylation, AARS1 acts as an intracellular lactate sensor and lactyltransferase, binding lactate with micromolar affinity and catalyzing ATP-dependent formation of lactyl-AMP that is transferred to lysine residues on diverse substrates [PMID:38653238, PMID:39322678, PMID:38512451]; the same active-site pocket underlies both serine misactivation and lactyltransferase activity [PMID:40479712]. Through this activity AARS1 lactylates p53 in its DNA-binding domain to block its phase separation, DNA binding, and transactivation [PMID:38653238], translocates to the nucleus to lactylate and activate the YAP-TEAD complex in a Hippo-pathway feedback loop [PMID:38512451], and modifies a broad substrate set—including histone H3K18, STAT1, BLM, Akt, NF-kB/p65, and Osterix—thereby linking lactate metabolism to immune signaling, DNA repair, autophagy, and transcriptional programs in cancer and metabolic disease [PMID:40634292, PMID:40987895, PMID:41832952, PMID:40505545]. AARS1 mutations cause peripheral neuropathy (CMT2N) through both loss-of-function alleles that reduce tRNA charging and gain-of-function alleles, with certain CMT2N mutations inducing structural loosening of the aminoacylation domain that enables aberrant binding to neuropilin 1 [PMID:22009580, PMID:33753480, PMID:30124830]; additional loss-of-function variants underlie trichothiodystrophy, myeloneuropathy, and recurrent acute liver failure [PMID:33909043, PMID:25904691, PMID:33294374].","teleology":[{"year":2009,"claim":"Established the structural basis for why alanyl-tRNA synthetase misactivates serine, defining the inherent fidelity problem the enzyme must solve.","evidence":"Nine X-ray crystal structures with kinetic and mutational analysis of AlaRS","pmids":["20010690"],"confidence":"High","gaps":["Does not address how misactivation is resolved in vivo beyond the intrinsic editing site","Bacterial/structural focus, human-specific differences not resolved"]},{"year":2011,"claim":"Showed that a CMT2N disease mutation directly impairs the core aminoacylation function, linking peripheral neuropathy to loss of tRNA charging.","evidence":"In vitro aminoacylation assay and yeast complementation of p.Arg329His","pmids":["22009580"],"confidence":"High","gaps":["Does not explain tissue-specific neuronal vulnerability","Later work showed R329H is aminoacylation-normal as purified protein, complicating the loss-of-function model"]},{"year":2016,"claim":"Revealed that the C-Ala domain has been repurposed in humans into a DNA-binding module, hinting at non-canonical functions beyond translation.","evidence":"Crystal structures of human C-Ala plus in vitro DNA binding assay","pmids":["27911835"],"confidence":"High","gaps":["Cellular role of C-Ala DNA binding not established","No in vivo phenotype tied to this activity"]},{"year":2017,"claim":"Defined a secondary cellular checkpoint for AlaRS mischarging errors, showing fidelity depends on a trans-acting deacylase beyond the synthetase's own editing.","evidence":"In vitro deacylation kinetics and genetic epistasis of DTD knockout in an AlaRS editing-defective E. coli background","pmids":["28362257"],"confidence":"High","gaps":["Demonstrated in bacteria; human DTD-AARS1 interplay not directly tested","Does not address glycine vs serine error rates in human cells"]},{"year":2018,"claim":"Resolved that CMT2N includes both hypomorphic and hypermorphic alleles and that a structural-loosening mechanism enables an aberrant gain-of-function interaction with neuropilin 1.","evidence":"Yeast complementation, aminoacylation assays, zebrafish models, plus biophysical/structural mapping and patient-cell Co-IP of the AlaRS-Nrp1 interaction","pmids":["30124830","33753480","30261202"],"confidence":"High","gaps":["How Nrp1 binding causes neurodegeneration mechanistically is unresolved","Relationship between mislocalization, gain-of-function binding, and charging defects not unified"]},{"year":2024,"claim":"Discovered the moonlighting function: AARS1 is a lactate sensor and lactyltransferase that forms lactyl-AMP and transfers lactyl groups to lysines, redirecting lactate metabolism into signaling and epigenetic regulation.","evidence":"In vitro enzymatic reconstitution of lactylation, lactate binding assays, and proteomics, replicated across labs; genetic code expansion and knock-in mice for the paralogous mechanism","pmids":["38653238","39322678","38512451"],"confidence":"High","gaps":["Full substrate repertoire and selectivity rules not defined","Regulation of nuclear translocation versus cytoplasmic charging not resolved"]},{"year":2024,"claim":"Connected AARS1 lactyltransferase activity to specific transcriptional outputs by showing lactylation inactivates p53 and activates YAP-TEAD in a Hippo feedback loop.","evidence":"Constitutively lactylated p53 variants with DNA-binding and phase-separation assays; nuclear translocation imaging, reporter assays, and loss-of-function in gastric cancer cells","pmids":["38653238","38512451"],"confidence":"High","gaps":["Stoichiometry of endogenous lactylation on these targets not quantified","Whether p53 and YAP-TEAD effects co-occur in the same tumors is untested"]},{"year":2025,"claim":"Expanded the lactylation substrate network into DNA repair, immune signaling, lipid metabolism, and transcription, establishing AARS1 as a broad metabolic-signaling hub in disease.","evidence":"Co-IP, lactylome/mass spectrometry, site-directed lysine mutations, ubiquitination assays, and conditional knockout mouse models across BLM, STAT1/H3K18, Akt/p65, and Osterix","pmids":["40634292","40987895","42215867","40505545","41832952"],"confidence":"Medium","gaps":["Most substrate links rest on single-lab studies","Direct versus indirect lactylation not always distinguished from cellular lactate effects"]},{"year":2025,"claim":"Mapped the mechanistic link between the lactate-binding pocket and serine misactivation, showing a single residue change abolishes both activities.","evidence":"Crystal structure of a pre-activation state plus aminoacylation and lactyltransferase kinetics of an L219M mutant in a bacterial AlaRS ortholog","pmids":["40479712"],"confidence":"Medium","gaps":["Bacterial ortholog; human pocket equivalence inferred not proven","Does not establish physiological lactyltransferase regulation in human cells"]},{"year":2025,"claim":"Systematically classified recessive AARS1 disease variants and revealed that some can act dominant-negatively, refining genotype-phenotype models.","evidence":"Side-by-side humanized yeast complementation of reported variants with dominant-negative testing (preprint)","pmids":["38979321"],"confidence":"Medium","gaps":["Preprint, single lab","Yeast does not capture human neuronal or lactyltransferase phenotypes"]},{"year":null,"claim":"How AARS1 partitions between aminoacylation and lactyltransferase functions, and what controls its nuclear translocation and substrate selection in different tissues, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model linking charging defects, Nrp1 gain-of-function, and lactylation in CMT2N","Endogenous lactylation stoichiometry and physiological triggers undefined","Substrate specificity determinants of the lactyltransferase activity unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,3,14]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,14]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[4,5,10]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[4,5,9]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[0,5]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[4,5]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[8]},{"term_id":"GO:0140299","term_label":"molecular sensor activity","supporting_discovery_ids":[0,3]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[11]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[11]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[4,5,10]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,3,20]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[14]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[16,17]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[4,7,13]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,21]}],"complexes":[],"partners":["NRP1","YAP1","TEAD","STAT1","BLM","AKT1","RELA"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P49588","full_name":"Alanine--tRNA ligase, cytoplasmic","aliases":["Alanyl-tRNA synthetase","AlaRS","Protein lactyltransferase AARS1","Renal carcinoma antigen NY-REN-42"],"length_aa":968,"mass_kda":106.8,"function":"Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala) (PubMed:27622773, PubMed:27911835, PubMed:28493438, PubMed:33909043). Also edits incorrectly charged tRNA(Ala) via its editing domain (PubMed:27622773, PubMed:27911835, PubMed:28493438, PubMed:29273753). In presence of high levels of lactate, also acts as a protein lactyltransferase that mediates lactylation of lysine residues in target proteins, such as TEAD1, TP53/p53 and YAP1 (PubMed:38512451, PubMed:38653238). Protein lactylation takes place in a two-step reaction: lactate is first activated by ATP to form lactate-AMP and then transferred to lysine residues of target proteins (PubMed:38512451, PubMed:38653238, PubMed:39322678). Acts as an inhibitor of TP53/p53 activity by catalyzing lactylation of TP53/p53 (PubMed:38653238). Acts as a positive regulator of the Hippo pathway by mediating lactylation of TEAD1 and YAP1 (PubMed:38512451)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/P49588/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/AARS1","classification":"Common Essential","n_dependent_lines":1208,"n_total_lines":1208,"dependency_fraction":1.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/AARS1","total_profiled":1310},"omim":[{"mim_id":"619692","title":"TRICHOTHIODYSTROPHY 9, NONPHOTOSENSITIVE; TTD9","url":"https://www.omim.org/entry/619692"},{"mim_id":"619691","title":"TRICHOTHIODYSTROPHY 8, NONPHOTOSENSITIVE; TTD8","url":"https://www.omim.org/entry/619691"},{"mim_id":"619661","title":"LEUKOENCEPHALOPATHY, HEREDITARY DIFFUSE, WITH SPHEROIDS 2; HDLS2","url":"https://www.omim.org/entry/619661"},{"mim_id":"616339","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 29; DEE29","url":"https://www.omim.org/entry/616339"},{"mim_id":"615259","title":"METHYLTRANSFERASE 21C, AARS1 LYSINE; METTL21C","url":"https://www.omim.org/entry/615259"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/AARS1"},"hgnc":{"alias_symbol":["CMT2N","AlaRS"],"prev_symbol":["AARS"]},"alphafold":{"accession":"P49588","domains":[{"cath_id":"3.30.930.10","chopping":"8-260","consensus_level":"medium","plddt":92.6284,"start":8,"end":260},{"cath_id":"-","chopping":"264-382","consensus_level":"high","plddt":92.0695,"start":264,"end":382},{"cath_id":"-","chopping":"402-459","consensus_level":"medium","plddt":73.1526,"start":402,"end":459},{"cath_id":"2.40.30.130","chopping":"468-594","consensus_level":"high","plddt":89.8057,"start":468,"end":594},{"cath_id":"3.30.980.10","chopping":"613-744","consensus_level":"medium","plddt":92.2156,"start":613,"end":744},{"cath_id":"3.10.310.40","chopping":"854-964","consensus_level":"high","plddt":92.4933,"start":854,"end":964}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P49588","model_url":"https://alphafold.ebi.ac.uk/files/AF-P49588-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P49588-F1-predicted_aligned_error_v6.png","plddt_mean":90.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=AARS1","jax_strain_url":"https://www.jax.org/strain/search?query=AARS1"},"sequence":{"accession":"P49588","fasta_url":"https://rest.uniprot.org/uniprotkb/P49588.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P49588/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P49588"}},"corpus_meta":[{"pmid":"38653238","id":"PMC_38653238","title":"Alanyl-tRNA 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\"AARS1 functions as a lactate sensor that binds lactate with micromolar affinity and catalyzes ATP-dependent formation of lactyl-AMP, which is then transferred to lysine acceptor residues on target proteins, establishing AARS1 as a bona fide lactyltransferase enzyme.\",\n      \"method\": \"In vitro biochemical assay (ATP-dependent lactylation), binding assays, proteomics\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro enzymatic reconstitution of lactylation activity demonstrated in two independent labs (PMID:38653238 and PMID:39322678) with multiple orthogonal methods\",\n      \"pmids\": [\"38653238\", \"39322678\", \"38512451\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"AARS1 lactylates p53 at lysine 120 and lysine 139 in the DNA-binding domain, hindering p53 liquid-liquid phase separation, DNA binding, and transcriptional activation, as demonstrated using constitutively lactylated p53 variants.\",\n      \"method\": \"Proteomics, generation of constitutively lactylated lysine variants, in vitro DNA binding assays, phase separation assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro functional validation with engineered p53 variants plus proteomics, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"38653238\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"AARS2 (the mitochondrial paralog) associates with cGAS and mediates its lactylation; lactylation at a specific N-terminal site abolishes cGAS liquid-like phase separation and DNA sensing in vitro and in vivo, as confirmed by a genetic code expansion lactyl-lysine incorporation system and knock-in mice.\",\n      \"method\": \"Co-immunoprecipitation, genetic code expansion (orthogonal system for lactyl-lysine incorporation), knock-in mouse models, in vitro phase separation assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstitution of lactylation activity, genetic knock-in validation in mice, multiple orthogonal methods in a single rigorous study; note this finding is primarily about AARS2 but the paper establishes the shared lactylation mechanism for both AARS1 and AARS2\",\n      \"pmids\": [\"39322678\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"AARS1 senses intracellular lactate and translocates into the nucleus, where it lactylates and activates the YAP-TEAD complex; AARS1 itself is a Hippo target gene forming a positive-feedback loop with YAP-TEAD to promote gastric cancer cell proliferation.\",\n      \"method\": \"In vitro lactyltransferase assay, nuclear translocation imaging, reporter assays, loss-of-function studies\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — direct in vitro lactyltransferase activity demonstrated, nuclear translocation documented, feedback loop established by multiple methods in a single lab\",\n      \"pmids\": [\"38512451\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The CMT2N disease-associated p.Arg329His mutation in AARS1 severely reduces aminoacylation (tRNA charging) enzyme activity, as demonstrated by aminoacylation assays and yeast viability complementation assays.\",\n      \"method\": \"In vitro aminoacylation assay, yeast complementation assay\",\n      \"journal\": \"Human mutation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct in vitro enzymatic assay plus yeast functional complementation, replicated in multiple families and independently confirmed\",\n      \"pmids\": [\"22009580\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"AlaRS (AARS1) has an inherent structural dilemma in amino acid recognition: an acidic residue required to pin down the alpha-amino group of alanine serendipitously interacts with the serine OH, explaining why serine is misactivated. Nine crystal structures and kinetic/mutational analysis provided the mechanistic basis.\",\n      \"method\": \"X-ray crystallography (9 structures), kinetic assays, site-directed mutagenesis\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple crystal structures combined with kinetic and mutational analysis in one rigorous study\",\n      \"pmids\": [\"20010690\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"AARS1 variants causing trichothiodystrophy result in instability of the alanyl-tRNA synthetase protein and a reduced rate of tRNA charging (aminoacylation), as demonstrated by functional studies in patient-derived skin fibroblasts.\",\n      \"method\": \"tRNA charging activity assay in patient fibroblasts, protein stability assessment\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct enzymatic activity measurement in patient cells, two orthogonal readouts (protein stability and tRNA charging), single lab\",\n      \"pmids\": [\"33909043\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CMT2N-associated mutations in the aminoacylation domain of AlaRS (including R329H) induce structural loosening of the aminoacylation domain, enabling aberrant gain-of-function binding to neuropilin 1 (Nrp1); this interaction was confirmed in patient samples and the b1b2 domains of Nrp1 are responsible. Notably, R329H is aminoacylation-normal as a purified protein in vitro.\",\n      \"method\": \"X-ray crystallography, small-angle X-ray scattering, hydrogen-deuterium exchange (HDX), switchSENSE hydrodynamic diameter, protease digestion, Co-immunoprecipitation in patient cells\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple biophysical and structural methods plus patient-sample validation confirming AlaRS-Nrp1 interaction, single rigorous study with extensive orthogonal evidence\",\n      \"pmids\": [\"33753480\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Crystal structures of human C-Ala (the C-terminal domain of AlaRS) revealed that sequence divergence from prokaryotic C-Ala reshaped the domain architecture, forming a dimer interface with a DNA-binding groove; direct DNA binding by human C-Ala (but not bacterial C-Ala) was demonstrated, indicating a repurposing of this domain in higher organisms.\",\n      \"method\": \"X-ray crystallography (two crystal forms of human C-Ala), small-angle X-ray scattering, in vitro DNA binding assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures combined with functional DNA binding assay in a single rigorous study\",\n      \"pmids\": [\"27911835\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"D-aminoacyl-tRNA deacylase (DTD) edits mischarged Gly-tRNAAla species (generated by AARS1 mischarging) four orders of magnitude more efficiently than AARS1's own editing activity; DTD knockout in an AlaRS editing-defective background causes pronounced toxicity in E. coli, establishing DTD as a secondary cellular checkpoint for glycine mischarging by AlaRS.\",\n      \"method\": \"In vitro editing/deacylation kinetic assays, genetic epistasis (DTD knockout in AlaRS editing-defective background), in vivo toxicity rescue by alanine supplementation\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro kinetic reconstitution plus genetic epistasis with multiple controls\",\n      \"pmids\": [\"28362257\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CMT2N-associated AARS1 mutations include both loss-of-function (hypomorphic: p.Ser627Leu, p.Arg326Trp) and gain-of-function (hypermorphic: p.Glu337Lys) alleles; yeast complementation demonstrated the functional class of each, and aminoacylation assays confirmed p.Glu337Lys increases tRNA charging velocity. All three caused neural abnormalities in zebrafish.\",\n      \"method\": \"Yeast complementation assay, in vitro aminoacylation assay, zebrafish expression model\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct enzymatic assay plus yeast complementation plus zebrafish model, multiple orthogonal methods in a single lab\",\n      \"pmids\": [\"30124830\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The CMT2N-associated N71Y mutation of AARS1 causes mislocalization of the protein to lysosomes (instead of cytoplasm) in COS-7 cells, and expression of this mutant in N1E-115 neuronal cells inhibits neurite process growth; this inhibition is reversed by pretreatment with valproic acid.\",\n      \"method\": \"Immunofluorescence localization, neuronal process growth assay, pharmacological rescue\",\n      \"journal\": \"Neuroscience research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization experiment and functional neuronal phenotype, two cell line models, single lab\",\n      \"pmids\": [\"30261202\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"A novel AARS1 p.Gly102Arg mutation fails to complement yeast lacking AARS function, demonstrating the mutation is damaging to tRNA synthetase activity; affected individuals present with myeloneuropathy.\",\n      \"method\": \"Yeast complementation assay\",\n      \"journal\": \"Neurology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — yeast complementation is a functional assay but single method, single lab\",\n      \"pmids\": [\"25904691\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"AARS1 deficiency variants (p.Leu298Gln; p.Arg751Gly) cause decreased aminoacylation (tRNA charging) enzymatic activity in patient-derived fibroblasts, associated with recurrent acute liver failure.\",\n      \"method\": \"Enzymatic activity assay in patient fibroblasts\",\n      \"journal\": \"Molecular genetics and metabolism reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct enzymatic activity measurement in patient cells, single lab, single method\",\n      \"pmids\": [\"33294374\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"AARS1 lactylates BLM helicase at Lys24, improving BLM protein stability by inhibiting MIB1-mediated ubiquitination and increasing its interaction with DNA repair factors, thereby promoting DNA end resection and homologous recombination repair, which drives chemoresistance to anthracyclines.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, global lactylome profiling, Lys24 mutation (delactylation), ubiquitination assay\",\n      \"journal\": \"Signal transduction and targeted therapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, mass spectrometry, mutation-based functional validation, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"40634292\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"AARS1 lactylates histone H3K18 and STAT1, and interacts with STAT1 to jointly regulate ELOVL5 transcription, inducing lipid peroxidation and ferroptosis in diabetic nephropathy; β-alanine inhibits AARS1-mediated lactylation and attenuates ferroptosis in model mice.\",\n      \"method\": \"Co-immunoprecipitation, transcriptomic and lipidomic analyses, AARS1 heterozygous mouse model, molecular biological assays\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for AARS1-STAT1 interaction, in vivo mouse model, multiple readouts; single lab\",\n      \"pmids\": [\"40987895\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"AARS1 lactylates STAT1 at K193, inhibiting its binding to JAK2 and phosphorylation, thereby disrupting IFN-γ signaling and reducing downstream chemokine expression (CXCL9/10/11), facilitating tumor immune escape; a cell-penetrating peptide targeting K193 lactylation restored IFN-γ responsiveness.\",\n      \"method\": \"Co-immunoprecipitation, phosphorylation assays, loss-of-function studies, peptide inhibitor\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding/phosphorylation assays, mechanistic peptide rescue, single lab\",\n      \"pmids\": [\"41832952\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"AARS1 directly lactylates Akt and the NF-κB subunit p65, enhancing their phosphorylation and activation, which impairs autophagy, promotes inflammation and tubular injury in diabetic kidney disease; kidney-specific Aars1 knockout or β-alanine treatment reduced these effects in mouse models.\",\n      \"method\": \"CUT and Tag, ChIP assays, luciferase reporter assays, CRISPR/Cas9 KO cells, kidney-specific knockout mice, streptozotocin and db/db diabetic models\",\n      \"journal\": \"Cellular & molecular biology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct lactylation of substrates with in vivo KO validation, multiple methods, single lab\",\n      \"pmids\": [\"42215867\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A single-point mutation L219M in AlaRS (from Methylomonas sp.) eliminates serine misactivation; structural analysis revealed that flexibility of Val204 is key to blocking serine binding in the mutant. The same mutation also eliminates the enzyme's inherent lactyltransferase activity, linking the lactate-binding/activation pocket to the serine misactivation mechanism.\",\n      \"method\": \"X-ray crystallography (pre-activation state structure), in vitro aminoacylation kinetic assays, in vitro lactyltransferase assay, site-directed mutagenesis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — crystal structure plus in vitro assays, bacterial ortholog, single lab\",\n      \"pmids\": [\"40479712\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"AARS1 catalyzes lactylation of ATRIP at K127 in neuronal processes during sepsis, triggering ATRIP-ATR complex formation and pathway activation independent of DNA damage, causing excessive autophagy, synaptic dysfunction and neuronal process injury; L-alanine competitively inhibits lactate binding to AARS1 and suppresses this signaling.\",\n      \"method\": \"In vivo CLP sepsis mouse model, AARS1 knockdown, ATR inhibitor, lactylation site mapping, behavioral assays\",\n      \"journal\": \"Brain, behavior, and immunity\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo mouse model with pharmacological and genetic inhibition, site-specific lactylation, single lab\",\n      \"pmids\": [\"41713664\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"AARS1 lactylates Osterix (Osx) transcription factor, increasing its binding to target gene promoters and promoting interaction with WDR5, which facilitates H3K4 tri-methylation on downstream target genes, enhancing osteoblast differentiation; silencing of AARS1 impaired alkaline phosphatase activity and mineralized nodule formation.\",\n      \"method\": \"Chromatin immunoprecipitation, Co-immunoprecipitation, loss-of-function knockdown, ALP activity assay, Alizarin Red staining\",\n      \"journal\": \"Acta histochemica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and Co-IP with functional osteoblast differentiation assays, single lab\",\n      \"pmids\": [\"40505545\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"AARS1 mediates lactylation of AKR1B10 at K173, stabilizing AKR1B10 by blocking MIB1-mediated ubiquitin-proteasomal degradation; stabilized AKR1B10 interacts with LDHA, promotes LDHA Y10 phosphorylation and glycolytic lactate production, which drives H3K18 lactylation and transcriptional upregulation of LDHA, forming a self-reinforcing circuit driving lenvatinib resistance in HCC.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, ubiquitination assay, western blot, functional metabolic assays (Seahorse XF)\",\n      \"journal\": \"Clinical and translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, MS-based PTM mapping, ubiquitination assay, single lab\",\n      \"pmids\": [\"41454479\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Comprehensive humanized yeast model assessment of AARS1 recessive disease variants showed the majority cause variable loss-of-function effects; K81T AARS1 demonstrated both loss-of-function and dominant-negative effects, indicating certain AARS1 variants can cause both dominant and recessive phenotypes.\",\n      \"method\": \"Humanized yeast complementation assay (side-by-side comparison of all reported recessive missense variants)\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic yeast complementation with dominant-negative testing, preprint, single lab\",\n      \"pmids\": [\"38979321\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"AARS1 promotes endometriosis by lactylating Snail1 to maintain its protein stability, enhancing epithelial-to-mesenchymal transition in endometriotic stromal cells.\",\n      \"method\": \"Co-immunoprecipitation, loss-of-function knockdown, cell proliferation/migration/invasion assays\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP plus functional cellular assays, single lab, limited mechanistic detail in abstract\",\n      \"pmids\": [\"40815826\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"AARS1 is a bifunctional enzyme that (1) performs its canonical role as an alanyl-tRNA synthetase, charging tRNA with alanine via an ATP-dependent mechanism with a G3:U70 tRNA recognition element and an editing domain that proofreads serine and glycine mischarging, and (2) moonlights as an intracellular lactate sensor and lactyltransferase that binds lactate with micromolar affinity, catalyzes formation of lactyl-AMP, and transfers the lactyl moiety to lysine residues on diverse substrates including p53, YAP-TEAD, cGAS, BLM, STAT1, Akt, NF-κB/p65, and histone H3K18, thereby linking cellular lactate metabolism to epigenetic regulation, immune signaling, DNA repair, and oncogenesis; CMT2N-associated mutations in its aminoacylation domain induce structural loosening that enables aberrant gain-of-function binding to neuropilin 1 (Nrp1), while loss-of-function mutations reduce tRNA charging activity causing peripheral neuropathy or multi-system disease.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"AARS1 is a bifunctional protein that couples canonical protein synthesis to lactate-driven signaling and epigenetic control [#0, #3]. In its housekeeping role it is an alanyl-tRNA synthetase whose active site has an inherent amino-acid recognition dilemma: an acidic residue that pins the alpha-amino group of alanine also engages the serine hydroxyl, accounting for serine misactivation, which is corrected by an editing function and backed up cellularly by the independent deacylase DTD that clears mischarged Gly-tRNA-Ala [#5, #9]. The C-terminal C-Ala domain has been structurally repurposed in humans to form a dimer interface with a DNA-binding groove [#8]. Beyond aminoacylation, AARS1 acts as an intracellular lactate sensor and lactyltransferase, binding lactate with micromolar affinity and catalyzing ATP-dependent formation of lactyl-AMP that is transferred to lysine residues on diverse substrates [#0]; the same active-site pocket underlies both serine misactivation and lactyltransferase activity [#18]. Through this activity AARS1 lactylates p53 in its DNA-binding domain to block its phase separation, DNA binding, and transactivation [#1], translocates to the nucleus to lactylate and activate the YAP-TEAD complex in a Hippo-pathway feedback loop [#3], and modifies a broad substrate set—including histone H3K18, STAT1, BLM, Akt, NF-kB/p65, and Osterix—thereby linking lactate metabolism to immune signaling, DNA repair, autophagy, and transcriptional programs in cancer and metabolic disease [#14, #15, #16, #20]. AARS1 mutations cause peripheral neuropathy (CMT2N) through both loss-of-function alleles that reduce tRNA charging and gain-of-function alleles, with certain CMT2N mutations inducing structural loosening of the aminoacylation domain that enables aberrant binding to neuropilin 1 [#4, #7, #10]; additional loss-of-function variants underlie trichothiodystrophy, myeloneuropathy, and recurrent acute liver failure [#6, #12, #13].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Established the structural basis for why alanyl-tRNA synthetase misactivates serine, defining the inherent fidelity problem the enzyme must solve.\",\n      \"evidence\": \"Nine X-ray crystal structures with kinetic and mutational analysis of AlaRS\",\n      \"pmids\": [\"20010690\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not address how misactivation is resolved in vivo beyond the intrinsic editing site\", \"Bacterial/structural focus, human-specific differences not resolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Showed that a CMT2N disease mutation directly impairs the core aminoacylation function, linking peripheral neuropathy to loss of tRNA charging.\",\n      \"evidence\": \"In vitro aminoacylation assay and yeast complementation of p.Arg329His\",\n      \"pmids\": [\"22009580\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not explain tissue-specific neuronal vulnerability\", \"Later work showed R329H is aminoacylation-normal as purified protein, complicating the loss-of-function model\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Revealed that the C-Ala domain has been repurposed in humans into a DNA-binding module, hinting at non-canonical functions beyond translation.\",\n      \"evidence\": \"Crystal structures of human C-Ala plus in vitro DNA binding assay\",\n      \"pmids\": [\"27911835\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular role of C-Ala DNA binding not established\", \"No in vivo phenotype tied to this activity\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined a secondary cellular checkpoint for AlaRS mischarging errors, showing fidelity depends on a trans-acting deacylase beyond the synthetase's own editing.\",\n      \"evidence\": \"In vitro deacylation kinetics and genetic epistasis of DTD knockout in an AlaRS editing-defective E. coli background\",\n      \"pmids\": [\"28362257\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Demonstrated in bacteria; human DTD-AARS1 interplay not directly tested\", \"Does not address glycine vs serine error rates in human cells\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Resolved that CMT2N includes both hypomorphic and hypermorphic alleles and that a structural-loosening mechanism enables an aberrant gain-of-function interaction with neuropilin 1.\",\n      \"evidence\": \"Yeast complementation, aminoacylation assays, zebrafish models, plus biophysical/structural mapping and patient-cell Co-IP of the AlaRS-Nrp1 interaction\",\n      \"pmids\": [\"30124830\", \"33753480\", \"30261202\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How Nrp1 binding causes neurodegeneration mechanistically is unresolved\", \"Relationship between mislocalization, gain-of-function binding, and charging defects not unified\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Discovered the moonlighting function: AARS1 is a lactate sensor and lactyltransferase that forms lactyl-AMP and transfers lactyl groups to lysines, redirecting lactate metabolism into signaling and epigenetic regulation.\",\n      \"evidence\": \"In vitro enzymatic reconstitution of lactylation, lactate binding assays, and proteomics, replicated across labs; genetic code expansion and knock-in mice for the paralogous mechanism\",\n      \"pmids\": [\"38653238\", \"39322678\", \"38512451\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full substrate repertoire and selectivity rules not defined\", \"Regulation of nuclear translocation versus cytoplasmic charging not resolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connected AARS1 lactyltransferase activity to specific transcriptional outputs by showing lactylation inactivates p53 and activates YAP-TEAD in a Hippo feedback loop.\",\n      \"evidence\": \"Constitutively lactylated p53 variants with DNA-binding and phase-separation assays; nuclear translocation imaging, reporter assays, and loss-of-function in gastric cancer cells\",\n      \"pmids\": [\"38653238\", \"38512451\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry of endogenous lactylation on these targets not quantified\", \"Whether p53 and YAP-TEAD effects co-occur in the same tumors is untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Expanded the lactylation substrate network into DNA repair, immune signaling, lipid metabolism, and transcription, establishing AARS1 as a broad metabolic-signaling hub in disease.\",\n      \"evidence\": \"Co-IP, lactylome/mass spectrometry, site-directed lysine mutations, ubiquitination assays, and conditional knockout mouse models across BLM, STAT1/H3K18, Akt/p65, and Osterix\",\n      \"pmids\": [\"40634292\", \"40987895\", \"42215867\", \"40505545\", \"41832952\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Most substrate links rest on single-lab studies\", \"Direct versus indirect lactylation not always distinguished from cellular lactate effects\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Mapped the mechanistic link between the lactate-binding pocket and serine misactivation, showing a single residue change abolishes both activities.\",\n      \"evidence\": \"Crystal structure of a pre-activation state plus aminoacylation and lactyltransferase kinetics of an L219M mutant in a bacterial AlaRS ortholog\",\n      \"pmids\": [\"40479712\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Bacterial ortholog; human pocket equivalence inferred not proven\", \"Does not establish physiological lactyltransferase regulation in human cells\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Systematically classified recessive AARS1 disease variants and revealed that some can act dominant-negatively, refining genotype-phenotype models.\",\n      \"evidence\": \"Side-by-side humanized yeast complementation of reported variants with dominant-negative testing (preprint)\",\n      \"pmids\": [\"38979321\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, single lab\", \"Yeast does not capture human neuronal or lactyltransferase phenotypes\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How AARS1 partitions between aminoacylation and lactyltransferase functions, and what controls its nuclear translocation and substrate selection in different tissues, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model linking charging defects, Nrp1 gain-of-function, and lactylation in CMT2N\", \"Endogenous lactylation stoichiometry and physiological triggers undefined\", \"Substrate specificity determinants of the lactyltransferase activity unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 3, 14]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 14]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [4, 5, 10]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [4, 5, 9]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0140299\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [11]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4, 5, 10]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 3, 20]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [14]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [16, 17]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [4, 7, 13]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 21]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"NRP1\", \"YAP1\", \"TEAD\", \"STAT1\", \"BLM\", \"AKT1\", \"RELA\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}