Affinage

ACSS3

Acyl-CoA synthetase short-chain family member 3, mitochondrial · UniProt Q9H6R3

Length
686 aa
Mass
74.8 kDa
Annotated
2026-06-09
41 papers in source corpus 11 papers cited in narrative 11 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ACSS3 is a mitochondrial acyl-CoA synthetase that serves as the primary enzyme of propionate catabolism, activating propionate to propionyl-CoA in tissues such as liver and brown adipose tissue (PMID:28003429, PMID:35184387). Biochemical reconstitution with purified recombinant protein established it as a propionyl-CoA synthetase of the mitochondrial matrix that preferentially uses propionate (KM ~0.19 mM) and is induced in liver mitochondria during fasting (PMID:28003429). In brown adipose tissue ACSS3 resides on the inner mitochondrial membrane, and its loss in mice causes propionate accumulation in BAT and serum that drives adipocyte autophagy, producing obesity, glucose intolerance, and insulin resistance — phenotypes reversed by pharmacological autophagy inhibition (PMID:35184387). Beyond catabolic clearance, the propionyl-CoA ACSS3 generates feeds histone propionylation that upregulates lipid metabolism genes; this output operates downstream of an RPN11–METTL3 axis in which m6A-dependent ACSS3 induction promotes hepatic steatosis (PMID:39146936). ACSS3 additionally shapes lipid storage and tumor metabolism: it restrains lipid droplet deposition through stabilization of the coat protein PLIN3 in prostate cancer (PMID:33391508), supports lipogenic acetyl-CoA synthesis from acetate and histone acetylation under metabolic stress in bladder carcinoma (PMID:32398651), and limits p53-mediated ferroptosis via the SLC7A11/GPX4 axis in lung cancer (PMID:39961466). Its expression is directly repressed by the transcription factor BCL11A, linking ACSS3 to autophagy-dependent protection of epidermal cells from UVB damage (PMID:41039024).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2017 High

    Established the core enzymatic identity of ACSS3 — whether it was a bona fide acyl-CoA synthetase and what substrate it acts on — by direct biochemical reconstitution.

    Evidence Recombinant protein purification and in vitro enzymatic assay with substrate specificity profiling, subcellular fractionation, and siRNA knockdown in HepG2 cells

    PMID:28003429

    Open questions at the time
    • Tissue-wide contribution to whole-body propionate flux not assessed in vivo
    • Structural basis of propionate preference not determined
  2. 2022 High

    Placed ACSS3 at a defined physiological node by showing that its loss elevates propionate and drives adipocyte autophagy, connecting an enzymatic defect to systemic metabolic disease.

    Evidence Acss3 knockout mouse with metabolic phenotyping, tissue/serum propionate measurement, and pharmacological autophagy-inhibition rescue

    PMID:35184387

    Open questions at the time
    • Molecular mechanism by which propionate triggers autophagy not defined
    • Whether inner-membrane vs matrix localization reflects tissue-specific differences unresolved
  3. 2024 High

    Showed that ACSS3-derived propionyl-CoA acts as a signaling input to chromatin, linking its catabolic output to transcriptional control of lipid metabolism via histone propionylation downstream of RPN11-METTL3.

    Evidence Hepatocyte-specific RPN11 knockout mice, diet-induced NAFLD model, epistasis across RPN11-METTL3-ACSS3, histone propionylation assay, human NAFLD tissue

    PMID:39146936

    Open questions at the time
    • Which histone residues are propionylated and which genes they directly control not fully mapped
    • Direct enzymatic link between ACSS3 and the histone propionylation machinery not reconstituted
  4. 2021 Medium

    Extended ACSS3 function to lipid droplet regulation, showing it limits lipid storage and tumor progression through stabilizing the droplet coat protein PLIN3.

    Evidence Co-IP, lipid profiling, promoter methylation analysis, and xenograft assays in prostate cancer cells

    PMID:33391508

    Open questions at the time
    • Mechanism by which ACSS3 stabilizes PLIN3 not defined
    • Single-lab Co-IP without reciprocal validation
  5. 2020 Medium

    Demonstrated a second catalytic capacity — generation of lipogenic acetyl-CoA from acetate under metabolic stress feeding histone acetylation — broadening ACSS3 beyond propionate.

    Evidence Isotope tracing, knockdown with acetate utilization and histone acetylation readouts in bladder carcinoma cells

    PMID:32398651

    Open questions at the time
    • Relative in vitro efficiency on acetate vs propionate not quantified against [#0]
    • Single lineage tested
  6. 2025 Medium

    Connected ACSS3 to redox/cell-death control, showing its loss enhances p53 stability and ferroptosis via suppression of the SLC7A11/GPX4 axis.

    Evidence Loss- and gain-of-function in NSCLC cells with ferroptosis markers, p53 stability, mitochondrial function readouts, and in vivo tumor growth

    PMID:39961466

    Open questions at the time
    • Mechanism coupling ACSS3 enzymatic activity to p53 stabilization unclear
    • Whether effect requires catalytic function not tested
  7. 2025 Medium

    Identified an upstream transcriptional repressor, placing ACSS3 as a direct BCL11A target that mediates autophagy-dependent protection of epidermal cells from UVB damage.

    Evidence CRISPR/Cas9 BCL11A deletion, direct transcriptional target identification, autophagy/ROS/DNA-damage assays with pharmacological rescue

    PMID:41039024

    Open questions at the time
    • Direct BCL11A binding to the ACSS3 promoter not shown by ChIP in this entry
    • How elevated ACSS3 promotes autophagosome formation mechanistically unresolved
  8. 2023 Medium

    Implicated ACSS3 in fibrosis-associated metabolic homeostasis, with overexpression reprogramming lipid/carbohydrate flux and attenuating pulmonary fibrosis.

    Evidence Proteomics of IPF/bleomycin samples, ACSS3 overexpression in A549 cells with metabolite measurements, in vivo bleomycin model

    PMID:37979225

    Open questions at the time
    • Causal enzymatic basis for the metabolic shifts not isolated
    • Single-lab overexpression model

Open questions

Synthesis pass · forward-looking unresolved questions
  • How ACSS3's dual substrate usage (propionate vs acetate) is partitioned across tissues and metabolic states, and whether its diverse downstream phenotypes (autophagy, ferroptosis, lipid droplets) all flow from its acyl-CoA synthetase activity, remain unresolved.
  • No structural model relating substrate preference to context
  • Catalytic-dead mutant rescue not used to test whether non-metabolic phenotypes require enzyme activity
  • Reported Wnt/β-Catenin and Sox2 acetyltransferase roles rest on Low-confidence inhibitor/proteomics evidence

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016874 ligase activity 3 GO:0140098 catalytic activity, acting on RNA 2
Localization
GO:0005739 mitochondrion 2
Pathway
R-HSA-1430728 Metabolism 3
Partners

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2017 ACSS3 (rat ortholog) was demonstrated by molecular cloning and recombinant protein expression to be a propionyl-CoA synthetase localized to the mitochondrial matrix, preferentially utilizing propionate as a substrate with a KM of 0.19 mM. Knockdown of acss3 in HepG2 cells significantly decreased propionyl-CoA synthetase activity in cell lysates, and ACSS3 levels/activity were upregulated in liver mitochondria during fasting. Molecular cloning, recombinant protein purification from E. coli, in vitro enzymatic assay with substrate specificity profiling, subcellular fractionation of liver tissue, siRNA knockdown with enzymatic activity readout Journal of biochemistry High 28003429
2022 ACSS3 is the key enzyme for propionate catabolism in brown adipose tissue, located on the mitochondrial inner membrane. Knockout of Acss3 in mice reduces brown adipose tissue (BAT) mass, increases white adipose tissue (WAT) mass, leads to glucose intolerance and insulin resistance exacerbated by high-fat diet, and elevates propionate levels in BAT and serum. Elevated propionate drives adipocyte autophagy, and pharmacological inhibition of autophagy with hydroxychloroquine ameliorates obesity and insulin resistance in Acss3-/- mice. Acss3 knockout mouse model, metabolic phenotyping (glucose tolerance test, insulin tolerance test), propionate measurement in BAT and serum, pharmacological autophagy inhibition with hydroxychloroquine, cultured brown/white adipocyte propionate treatment with autophagy readout Clinical and translational medicine High 35184387
2024 RPN11 deubiquitinates and stabilizes METTL3, which enhances m6A modification and expression of ACSS3. ACSS3 in turn generates propionyl-CoA that upregulates lipid metabolism genes via histone propionylation. This RPN11-METTL3-ACSS3-histone propionylation pathway is activated in livers of NAFLD patients, and hepatocyte-specific RPN11 knockout protects mice from diet-induced liver steatosis. Hepatocyte-specific RPN11 knockout mice, diet-induced NAFLD model, mechanistic epistasis linking RPN11-METTL3-ACSS3, histone propionylation assay, human NAFLD liver samples Cell metabolism High 39146936
2021 ACSS3 represses prostate cancer progression by reducing lipid droplet (LD) deposits through regulating the stability of the LD coat protein perilipin 3 (PLIN3). Restoration of ACSS3 expression in PCa cells reduces LD deposits, promotes apoptosis by increasing endoplasmic reticulum (ER) stress, decreases de novo intratumoral androgen synthesis, and reverses enzalutamide resistance. Loss of ACSS3 expression in PCa is associated with gene promoter methylation. Co-IP, qRT-PCR, Western blotting, LC/MS lipid profiling, Oil Red O assay, TG and cholesterol measurement, Bisulfite genomic sequencing PCR and MSP for promoter methylation, CCK-8 and Transwell functional assays, xenograft tumorigenesis model in vivo Theranostics Medium 33391508
2023 ACSS3 participates in lipid and carbohydrate metabolic homeostasis in alveolar epithelial cells: overexpression downregulates CPT-1A (reducing fatty acid oxidation) and leads to lipid droplet accumulation, while enhancing glycolysis and extracellular lactic acid. ACSS3 increases succinyl-CoA production through propionic acid metabolism and decreases acetyl-CoA and ATP generation. Overexpression of Acss3 in vivo inhibited ECM deposition and attenuated ground-glass opacity in bleomycin-induced pulmonary fibrosis. Proteomic analysis of IPF patient and bleomycin-mouse samples, ACSS3 overexpression in A549 cells with metabolite measurements (succinyl-CoA, acetyl-CoA, ATP, lactic acid), CPT-1A protein measurement, lipid droplet staining, in vivo bleomycin fibrosis model with micro-CT Biochimica et biophysica acta. Molecular basis of disease Medium 37979225
2020 ACSS3 is responsible for lipogenic acetyl-CoA synthesis from acetate in bladder urothelial carcinoma (BLCA) cells under metabolic stress, is required for acetate utilization and histone acetylation, and promotes BLCA cell growth. Isotope tracing for lipogenic acetyl-CoA generation, ACSS3 knockdown with acetate utilization and histone acetylation readouts, cell growth assays Oncogenesis Medium 32398651
2025 ACSS3 knockdown in NSCLC cells promotes ferroptosis through transcriptional activation of the p53 pathway, which suppresses the SLC7A11/GPX4 axis. ACSS3 loss enhances p53 stability, and ACSS3 promotes tumor growth by inhibiting p53-mediated ferroptosis. ACSS3 knockdown led to mitochondrial contraction, increased ROS, and decreased mitochondrial membrane potential in NSCLC cells. ACSS3 knockdown and overexpression in NSCLC cells, in vitro and in vivo tumor growth assays, ferroptosis markers (SLC7A11, GPX4, ROS), p53 stability assessment, mitochondrial morphology/function measurements Experimental cell research Medium 39961466
2025 BCL11A transcriptionally represses ACSS3 as a direct target gene. BCL11A deficiency increases ACSS3 expression, promoting autophagosome formation and enhanced autophagy flux, which reduces DNA damage and ROS under UVB irradiation, protecting epidermal cells from UVB-induced death. This protective effect was blocked by pharmacological inhibition of autophagy or BCL11A overexpression. CRISPR/Cas9-mediated BCL11A deletion, ACSS3 identified as direct transcriptional target, autophagy flux assays, ROS measurement, DNA damage assays, pharmacological autophagy inhibition rescue Communications biology Medium 41039024
2025 ACSS3 modulates aerobic glycolysis and keloid fibroblast (KF) activity via the Wnt/β-Catenin pathway. Lentiviral overexpression of ACSS3 in KFs suppressed their activity, normalized glycolytic flux, and reduced levels of critical glycolytic enzymes, while ACSS3 knockdown had opposite effects that were reversed by the Wnt/β-Catenin inhibitor ICG-001. Lentiviral ACSS3 overexpression and knockdown in keloid fibroblasts, glycolytic flux measurement, glycolytic enzyme levels, pharmacological rescue with ICG-001 (Wnt/β-Catenin inhibitor), single-cell analysis Cellular signalling Low 40783148
2023 The EGFR/AKT pathway upregulates ACSS3 expression in glioblastoma (GBM) cells in an NF-κB-dependent manner, contributing to lipid remodeling and energy metabolism reprogramming in EGFR-activated GBM. Single-cell RNA sequencing and untargeted metabolomics of clinical GBM, EGFR/AKT pathway inhibition with MK-2206, NF-κB-dependent regulation of ACSS3 expression assessed in GBM cells, intracranial tumor model in vivo Cancer communications (London, England) Low 37920878
2024 ACSS3 functions as an acetyltransferase (or donor for acetyltransferase activity) contributing to CBP/p300-mediated acetylation of Sox2 at K75 in colorectal cancer cells, as identified by LC-MS-based proteomics binding partner analysis. LC-MS-based proteomics to identify binding partners of Sox2 in CRC cell lines, identification of ACSS3 as involved in K75 acetylation of Sox2 along with CBP/p300 Cancers Low 38473392

Source papers

Stage 0 corpus · 41 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2018 Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes. Proceedings of the National Academy of Sciences of the United States of America 171 30482855
2021 ACSS3 represses prostate cancer progression through downregulating lipid droplet-associated protein PLIN3. Theranostics 97 33391508
2019 Genome-wide by environment interaction studies of depressive symptoms and psychosocial stress in UK Biobank and Generation Scotland. Translational psychiatry 95 30718454
2014 Genome-wide association and biological pathway analysis for milk-fat composition in Danish Holstein and Danish Jersey cattle. BMC genomics 92 25511820
2017 Molecular cloning of rat acss3 and characterization of mammalian propionyl-CoA synthetase in the liver mitochondrial matrix. Journal of biochemistry 55 28003429
2013 A genome-wide association study of a sustained pattern of antidepressant response. Journal of psychiatric research 47 23726668
2023 Blockage of EGFR/AKT and mevalonate pathways synergize the antitumor effect of temozolomide by reprogramming energy metabolism in glioblastoma. Cancer communications (London, England) 42 37920878
2018 Mitochondrial Acetyl-CoA Synthetase 3 is Biosignature of Gastric Cancer Progression. Cancer medicine 41 29493120
2020 Extreme downregulation of chromosome Y and Alzheimer's disease in men. Neurobiology of aging 34 32147245
2016 Transcriptome Pathway Analysis of Pathological and Physiological Aldosterone-Producing Human Tissues. Hypertension (Dallas, Tex. : 1979) 33 27777363
2020 Genomic and transcriptomic landscape of conjunctival melanoma. PLoS genetics 32 33383577
2024 Amelioration of nonalcoholic fatty liver disease by inhibiting the deubiquitylating enzyme RPN11. Cell metabolism 28 39146936
2023 ACSS3 regulates the metabolic homeostasis of epithelial cells and alleviates pulmonary fibrosis. Biochimica et biophysica acta. Molecular basis of disease 27 37979225
2022 ACSS3 in brown fat drives propionate catabolism and its deficiency leads to autophagy and systemic metabolic dysfunction. Clinical and translational medicine 26 35184387
2021 Genome-Wide Association Studies Reveal Neurological Genes for Dog Herding, Predation, Temperament, and Trainability Traits. Frontiers in veterinary science 25 34368281
2020 Acetyl-CoA synthetase 3 promotes bladder cancer cell growth under metabolic stress. Oncogenesis 22 32398651
2012 A novel Acetyl-CoA synthetase short-chain subfamily member 1 (Acss1) gene indicates a dynamic history of paralogue retention and loss in vertebrates. Gene 20 22313524
2019 Conjugated linoleic acid (CLA)-induced milk fat depression: application of RNA-Seq technology to elucidate mammary gene regulation in dairy ewes. Scientific reports 15 30872673
2015 Alteration of factors associated with hepatic gluconeogenesis in response to acute lipopolysaccharide in dairy goat. Journal of animal science 11 26115264
2023 Integration of proteomics and network toxicology reveals the mechanism of mercury chloride induced hepatotoxicity, in mice and HepG2 cells. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association 10 37172713
2024 Sex-specific survival gene mutations are discovered as clinical predictors of clear cell renal cell carcinoma. Scientific reports 7 38982123
2023 A genome-wide association study for the fatty acid composition of breast meat in an F2 crossbred chicken population. Journal of animal science and technology 7 37970507
2024 A Comprehensive Understanding of Post-Translational Modification of Sox2 via Acetylation and O-GlcNAcylation in Colorectal Cancer. Cancers 5 38473392
2023 Single-nucleus RNA and ATAC sequencing uncovers the molecular and cellular characteristics in the musk gland of Chinese forest musk deer (Moschus berezovskii). FASEB journal : official publication of the Federation of American Societies for Experimental Biology 5 36583723
2020 Postmenopausal osteoporosis is a musculoskeletal disease with a common genetic trait which responds to strength training: a translational intervention study. Therapeutic advances in musculoskeletal disease 5 32536985
2024 Building Minimized Epigenetic Clock by iPlex MassARRAY Platform. Genes 3 38674360
2022 GBP5 and ACSS3: two potential biomarkers of high-grade ovarian cancer identified through downstream analysis of microarray data. Journal of biomolecular structure & dynamics 3 35502666
2022 Genome-wide assessment reveals a significant association between ACSS3 and physical activity. Genes, brain, and behavior 3 36510703
2017 Possible involvement of ACSS2 gene in alcoholism. Journal of neural transmission (Vienna, Austria : 1996) 3 28550509
2025 ACSS3 protein macromolecule regulates glycolysis in keloid through Wnt/β-catenin signaling pathway: Bioinformatics, machine learning, and experimental validation. Cellular signalling 2 40783148
2026 Recent advances in immunotherapy for gliomas: overcoming barriers and advancing precision strategies. Frontiers in immunology 1 41583467
2025 A Spatial Multi-Omic Framework Identifies Gliomas Permissive to TIL Expansion. bioRxiv : the preprint server for biology 1 40236001
2025 A Spatial Multi-Omic Framework Identifies Gliomas Permissive to TIL Expansion. Research square 1 40313763
2016 [Genome-wide analysis of DNA methylation in prostate cancer using the technology of Infinium HumanMethylation450 BeadChip (HM450)]. Voprosy onkologii 1 30444590
2026 Single-cell atlas reveals cellular heterogeneity and BMP5-mediated regulation of adipogenic differentiation in sheep adipose tissue. Communications biology 0 41565772
2026 Multi-omics analysis and experiments validate the tumor-suppressive role of mitochondrial lipid metabolism gene ACSM5 in lung adenocarcinoma and its impact on the immune microenvironment. Human genomics 0 41634895
2026 Decoding coronary artery calcification: metabolic reprogramming features and a promising circulating biomarker PXDN. Frontiers in cell and developmental biology 0 42039144
2025 ACSS3 promotes the tumorigenesis of non-small cell lung cancer via suppressing p53-mediated ferroptosis. Experimental cell research 0 39961466
2025 A new robust AI/ML based model for accurate forensic age estimation using DNA methylation markers. Forensic science, medicine, and pathology 0 40085291
2025 BCL11A deficiency protects epidermis from UVB-induced damage through promotion of autophagy. Communications biology 0 41039024
2022 Whole-exome sequencing of a patient with primary central nervous system T-cell lymphoma: Clinicopathological features and genomic profiling. Neuropathology : official journal of the Japanese Society of Neuropathology 0 35989547

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