GO:0003987 acetyl-CoA synthetase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0003987 acetyl-CoA synthetase activity catalyzes the ATP-dependent ligation of acetate and CoA to form acetyl-CoA, AMP, and diphosphate.
• ACSS2 is the nuclear/cytosolic acetyl-CoA synthetase that supports histone acetylation, memory formation, and cancer cell survival under metabolic stress.
• ACSS2 can also act as a lactyl-CoA synthetase, coupling to KAT2A to drive histone lactylation and tumor immune evasion.
• Dysregulated acetyl-CoA synthetase activity is implicated in cancer, sepsis-induced acute kidney injury, diabetic nephropathy, and Alzheimer's disease.
• CRISPR knockout, point mutation, knock-in, and overexpression models are essential to dissect ACSS2-dependent metabolic and epigenetic functions.
• EDITGENE provides end-to-end CRISPR cell model services and library screening to study acetyl-CoA synthetase activity in disease and development.
Description
Acetyl-CoA synthetase activity (GO:0003987) is a fundamental enzymatic function that converts acetate, ATP, and CoA into acetyl-CoA, AMP, and diphosphate. This reaction is critical for cellular metabolism because acetyl-CoA is a central metabolite that feeds the tricarboxylic acid cycle and serves as the acetyl donor for histone acetylation. In mammals, the acetyl-CoA synthetase family includes ACSS1, ACSS2, and ACSS3, with ACSS2 being the most studied nuclear/cytosolic isoform that supports acetate utilization under metabolic stress. The importance of this activity extends beyond basic metabolism: recent studies show that ACSS2 can act as a lactyl-CoA synthetase, coupling to KAT2A to promote histone lactylation and tumor immune evasion. Researchers study GO:0003987 to understand how cells adapt to nutrient limitation, how epigenetic states are maintained, and how dysregulation contributes to diseases such as cancer, kidney injury, and neurodegeneration. This article provides a research-grade overview of the mechanism, key genes, disease links, and experimental methods for investigating acetyl-CoA synthetase activity.
acetyl-CoA synthetase activity At A Glance
| GO ID | GO:0003987 |
|---|---|
| GO term | acetyl-CoA synthetase activity |
| Ontology | molecular_function |
| Synonym | acetate-CoA ligase activity; acetyl-CoA synthase activity; acetate thiokinase activity; ACS |
| Major function | Catalyzes ATP-dependent ligation of acetate and CoA to form acetyl-CoA, AMP, and diphosphate |
| Reaction | acetate + ATP + CoA = acetyl-CoA + AMP + diphosphate |
| Cofactors | ATP and CoA are required; Mg2+ is typically needed for ATP-dependent ligases |
| Subcellular localization | Cytosol, nucleus, and mitochondria depending on isoform (ACSS2 is nuclear/cytosolic) |
| Related genes | ACSS1, ACSS2, ACSS3 |
What Is GO:0003987?
Acetyl-CoA synthetase activity (GO:0003987) is defined by the Gene Ontology as the catalysis of the reaction: acetate + ATP + CoA = acetyl-CoA + AMP + diphosphate. In other words, it is an ATP-dependent ligase activity that activates acetate by forming a high-energy thioester bond with coenzyme A, producing acetyl-CoA. This activity is also known by synonyms such as acetate-CoA ligase, acetyl-CoA synthase, and acyl-activating enzyme activity. It belongs to the molecular_function ontology aspect and is distinct from other acetyl-CoA-producing enzymes like ATP-citrate lyase or pyruvate dehydrogenase.
Why Is acetyl-CoA synthetase activity Important in Cell Biology?
Acetyl-CoA synthetase activity is important because it provides a direct route for cells to generate acetyl-CoA from acetate, especially when glucose-derived acetyl-CoA is limited. This activity supports histone acetylation, memory formation, cancer cell survival under metabolic stress, and immune evasion through histone lactylation. Dysregulation of this activity is linked to multiple human diseases, including cancer, sepsis-induced acute kidney injury, diabetic nephropathy, and Alzheimer's disease. Therefore, understanding GO:0003987 is essential for researchers in metabolism, epigenetics, neuroscience, and oncology.
• Provides acetyl-CoA for histone acetylation and gene expression regulation.
• Supports cancer cell growth under metabolic stress by utilizing acetate.
• Drives histone lactylation and tumor immune evasion via ACSS2-KAT2A coupling.
• Regulates hippocampal memory and cognitive function.
• Mediates kidney injury in sepsis and diabetic nephropathy.
• Contributes to exhausted CD8+ T cell fate through nutrient-driven histone code.
• Implicated in Alzheimer's disease pathology and cognitive decline.
• Target for metabolic and epigenetic therapies in oncology and neurology.
Molecular Mechanism of acetyl-CoA synthetase activity
Substrate Binding and Acetyl-AMP Formation
In simple terms: The enzyme first grabs acetate and ATP to make a high-energy intermediate.
Acetyl-CoA synthetase binds acetate and ATP in its active site. The enzyme catalyzes the formation of acetyl-AMP, releasing pyrophosphate (diphosphate). This step activates the acetate carboxyl group for subsequent transfer to CoA.
CoA Transfer and Acetyl-CoA Release
In simple terms: The activated acetate is then handed over to CoA to form acetyl-CoA.
In the second step, the acetyl group from acetyl-AMP is transferred to the thiol group of coenzyme A, producing acetyl-CoA and releasing AMP. This two-step mechanism is characteristic of ATP-dependent ligases and is essential for generating acetyl-CoA from acetate.
Cofactors and Metal Requirements
In simple terms: The enzyme needs ATP and CoA, and often magnesium, to work.
Acetyl-CoA synthetase activity requires ATP and CoA as substrates. Like many ATP-dependent ligases, it typically requires divalent metal ions such as Mg2+ for ATP binding and catalysis. The reaction produces AMP and diphosphate as byproducts.
Isoform-Specific Localization and Function
In simple terms: Different versions of the enzyme work in different parts of the cell.
In mammals, ACSS2 is predominantly nuclear and cytosolic, where it supports histone acetylation by generating acetyl-CoA locally. ACSS1 is mitochondrial, and ACSS3 is also mitochondrial. This compartmentalization allows acetyl-CoA synthetase activity to fuel distinct metabolic and epigenetic processes.
Lactyl-CoA Synthetase Activity and Histone Lactylation
In simple terms: ACSS2 can also use lactate to make lactyl-CoA, which modifies histones.
Recent evidence shows that ACSS2 acts as a lactyl-CoA synthetase, coupling with KAT2A to function as a lactyltransferase for histone lactylation. This activity promotes tumor immune evasion, expanding the known functions of acetyl-CoA synthetase beyond acetate metabolism.
Key Genes Involved in GO:0003987 acetyl-CoA synthetase activity
The following genes encode enzymes with acetyl-CoA synthetase activity or closely related functions.
| Gene | Major Role | Research Relevance |
|---|---|---|
| ACSS2 | Cytosolic/nuclear acetyl-CoA synthetase; generates acetyl-CoA from acetate for histone acetylation and lipid synthesis | Cancer metabolism, epigenetics, memory, kidney injury, Alzheimer's disease |
| ACSS1 | Mitochondrial acetyl-CoA synthetase; utilizes acetate for TCA cycle | Metabolic studies, mitochondrial function |
| ACSS3 | Mitochondrial acetyl-CoA synthetase; role in lipid metabolism | Metabolic disorders, cancer |
| KAT2A | Histone acetyltransferase/lactyltransferase; couples with ACSS2 for histone lactylation | Tumor immune evasion, epigenetics |
| ATP-citrate lyase (ACLY) | Generates acetyl-CoA from citrate for histone acetylation | Links metabolism to histone acetylation |
| ACACA | Acetyl-CoA carboxylase; uses acetyl-CoA for fatty acid synthesis | Lipid metabolism |
| ACAT1 | Acetyl-CoA acetyltransferase; ketone body metabolism | Metabolic disorders |
| SLC25A1 | Mitochondrial citrate carrier; affects acetyl-CoA availability | Metabolic stress |
| SLC16A1 | Monocarboxylate transporter; acetate transport | Acetate utilization |
| SLC16A3 | Monocarboxylate transporter; lactate transport | Lactate metabolism |
| EP300 | Histone acetyltransferase; uses acetyl-CoA | Epigenetics |
| CREBBP | Histone acetyltransferase; uses acetyl-CoA | Epigenetics |
| HDAC1 | Histone deacetylase; removes acetyl groups | Epigenetics |
| HDAC2 | Histone deacetylase; removes acetyl groups | Epigenetics |
| SIRT1 | NAD+-dependent deacetylase; senses acetyl-CoA levels | Metabolism, aging |
| NF-κB | Transcription factor regulated by acetylation; involved in inflammation | Sepsis-induced AKI |
| KLF5 | Transcription factor upregulated by ACSS2 in sepsis-induced AKI | Kidney injury |
| BDNF | Neurotrophin regulated by histone acetylation; involved in memory | Alzheimer's disease, cognition |
How Is acetyl-CoA synthetase activity Regulated?
Acetyl-CoA synthetase activity is regulated at multiple levels. ACSS2 expression and activity are influenced by nutrient availability, metabolic stress, and hormonal signals. For example, under glucose limitation, ACSS2 promotes acetate utilization to maintain cancer cell growth. In the brain, ACSS2 regulates histone acetylation and hippocampal memory, and its activity is linked to cognitive function. ACSS2 is also regulated by post-translational modifications and interacts with KAT2A to modulate histone lactylation. Additionally, nutrient-driven histone code determines exhausted CD8+ T cell fates, implicating acetyl-CoA synthetase in immune cell regulation. In kidney injury, ACSS2 activation mediates damage through the KLF5/NF-κB pathway. These regulatory mechanisms highlight the integration of acetyl-CoA synthetase activity with cellular metabolism and gene expression.
acetyl-CoA synthetase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| ACSS2 | Cancer (metabolic stress, immune evasion) | Knockout or overexpression in cancer cell lines; xenograft models |
| ACSS2 | Sepsis-induced acute kidney injury | Knockout or overexpression in renal tubular cells; LPS-induced AKI mouse model |
| ACSS2 | Diabetic nephropathy | Knockout or overexpression in podocytes; streptozotocin-induced diabetic mouse model |
| ACSS2 | Alzheimer's disease | Knockout or overexpression in neurons; APP/PS1 mouse model |
| ACSS2 | CD8+ T cell exhaustion | Knockout or overexpression in T cells; chronic infection or tumor models |
Cancer Metabolism and Immune Evasion
ACSS2 promotes acetate utilization and maintains cancer cell growth under metabolic stress, making it a potential target for cancer therapy. Moreover, ACSS2 acts as a lactyl-CoA synthetase and couples with KAT2A to drive histone lactylation, which promotes tumor immune evasion. These findings link acetyl-CoA synthetase activity to both metabolic reprogramming and epigenetic immune regulation in cancer.
Kidney Injury and Inflammation
ACSS2 induces pyroptosis and inflammation of renal epithelial tubular cells in sepsis-induced acute kidney injury by upregulating the KLF5/NF-κB pathway. Activation of ACSS2 also mediates kidney injury in diabetic nephropathy. Therefore, acetyl-CoA synthetase activity is a potential therapeutic target for kidney diseases.
Neurodegeneration and Memory
Acetyl-CoA synthetase regulates histone acetylation and hippocampal memory, indicating a role in cognitive processes. ACSS2-dependent histone acetylation improves cognition in a mouse model of Alzheimer's disease. These studies suggest that modulating acetyl-CoA synthetase activity could have therapeutic potential in neurodegenerative disorders.
T Cell Exhaustion and Immunity
Nutrient-driven histone code determines exhausted CD8+ T cell fates, and acetyl-CoA synthetase activity contributes to this process. This links acetyl-CoA metabolism to immune cell function and potential immunotherapy strategies.
From acetyl-CoA synthetase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does ACSS2 loss affect cancer cell growth under metabolic stress? | ACSS2 knockout in cancer cell lines (e.g., HCT116, MCF7) |
| Does ACSS2 lactyl-CoA synthetase activity drive histone lactylation? | Point mutation of ACSS2 catalytic residues; knock-in of lactylation-deficient ACSS2 |
| Does ACSS2 overexpression improve cognition in Alzheimer's disease? | ACSS2 overexpression in neurons; APP/PS1 mouse model |
| Does ACSS2 mediate sepsis-induced acute kidney injury? | ACSS2 knockout or overexpression in renal tubular cells; LPS-induced AKI mouse model |
| Does ACSS2 regulate hippocampal memory? | ACSS2 knockout or overexpression in mouse hippocampus; behavioral tests |
| Does ACSS2 affect CD8+ T cell exhaustion? | ACSS2 knockout or overexpression in T cells; chronic LCMV infection model |
How to Study the acetyl-CoA synthetase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Enzymatic activity assay | Acetyl-CoA synthetase catalytic activity | Validate ACSS2 mutants and inhibitors |
| 13C-acetate tracing | Acetate utilization and acetyl-CoA production | Metabolic flux in cancer cells |
| Western blot | Histone acetylation/lactylation levels | Epigenetic changes |
| ChIP-seq | Genome-wide histone modification mapping | Identify target genes |
| RNA-seq | Transcriptional changes upon ACSS2 modulation | Pathway analysis |
| CRISPR knockout screening | Genes required for cell growth under metabolic stress | Identify synthetic lethal targets |
| Proteomics | Protein expression and interactions | ACSS2 interactome |
| Behavioral tests | Memory and cognition in mice | Hippocampal memory studies |
Enzymatic Activity Assays
Acetyl-CoA synthetase activity can be measured using coupled enzyme assays that detect AMP production or acetyl-CoA formation. These assays typically use acetate, ATP, and CoA as substrates and monitor the reaction spectrophotometrically or by HPLC. Such methods are essential to confirm the catalytic function of ACSS2 and its mutants.
Metabolic Flux Analysis
Stable isotope tracing with 13C-acetate can quantify acetate utilization and acetyl-CoA production in cells. This method helps assess how acetyl-CoA synthetase activity contributes to metabolic pathways under different conditions.
Histone Acetylation and Lactylation Profiling
Western blotting with antibodies against acetylated or lactylated histones can measure the impact of acetyl-CoA synthetase activity on epigenetic marks. Chromatin immunoprecipitation sequencing (ChIP-seq) can map these modifications genome-wide.
CRISPR Screening and Functional Genomics
Genome-wide CRISPR knockout or activation screens can identify genes that modulate acetyl-CoA synthetase activity or its downstream effects. These screens are powerful for discovering synthetic lethal interactions and resistance mechanisms.
How CRISPR Can Be Used to Study GO:0003987 acetyl-CoA synthetase activity
Knockout
CRISPR knockout of ACSS2 or other acetyl-CoA synthetase genes can abolish enzymatic activity, allowing researchers to study loss-of-function phenotypes in cancer, kidney injury, and memory. For example, ACSS2 knockout reduces cancer cell growth under metabolic stress and impairs hippocampal memory.
Point Mutation
Point mutations in the catalytic domain of ACSS2 can dissect specific functions, such as acetyl-CoA versus lactyl-CoA synthesis. For instance, mutating key residues can separate histone acetylation from lactylation effects.
Knock-in
Knock-in of tagged ACSS2 (e.g., FLAG or HA) enables localization and interaction studies. Knock-in of disease-associated variants can model human mutations affecting acetyl-CoA synthetase activity.
Overexpression
Overexpression of ACSS2 can enhance acetate utilization and histone acetylation, and has been shown to improve cognition in Alzheimer's disease models. It is also used to study tumor immune evasion.
How EDITGENE Supports acetyl-CoA synthetase activity Research
Researchers studying acetyl-CoA synthetase activity-related genes often need to determine whether a candidate gene is causally involved in metabolic, epigenetic, or disease phenotypes. CRISPR-based cell models provide a robust way to test gene function by creating precise knockouts, point mutations, knock-ins, or overexpression lines. EDITGENE offers a comprehensive suite of services to accelerate such studies.
Contact EDITGENE today to design your custom CRISPR model for acetyl-CoA synthetase activity research.
Frequently Asked Questions About acetyl-CoA synthetase activity
What is acetyl-CoA synthetase activity?
Acetyl-CoA synthetase activity (GO:0003987) is the enzymatic catalysis of the reaction acetate + ATP + CoA = acetyl-CoA + AMP + diphosphate, as defined by the Gene Ontology.
What genes are involved in acetyl-CoA synthetase activity?
The main genes are ACSS1, ACSS2, and ACSS3, which encode acetyl-CoA synthetases with different subcellular localizations.
What is the role of ACSS2 in cancer?
ACSS2 promotes acetate utilization and maintains cancer cell growth under metabolic stress, and it also drives histone lactylation for tumor immune evasion.
How is acetyl-CoA synthetase activity regulated?
It is regulated by nutrient availability, metabolic stress, and post-translational modifications, and it interacts with KAT2A to modulate histone lactylation.
What diseases are associated with acetyl-CoA synthetase activity?
It is implicated in cancer, sepsis-induced acute kidney injury, diabetic nephropathy, Alzheimer's disease, and T cell exhaustion.
What is the reaction catalyzed by acetyl-CoA synthetase?
The reaction is: acetate + ATP + CoA = acetyl-CoA + AMP + diphosphate.
How can I study acetyl-CoA synthetase activity in the lab?
You can use enzymatic activity assays, 13C-acetate tracing, histone modification profiling, and CRISPR knockout or overexpression models.
What is the difference between ACSS1 and ACSS2?
ACSS1 is mitochondrial and supports the TCA cycle, while ACSS2 is nuclear/cytosolic and provides acetyl-CoA for histone acetylation and lipid synthesis.
Does acetyl-CoA synthetase activity affect memory?
Yes, ACSS2 regulates histone acetylation and hippocampal memory, and its overexpression improves cognition in Alzheimer's disease models.
What CRISPR models are available for acetyl-CoA synthetase research?
EDITGENE offers knockout, point mutation, knock-in, and overexpression cell models for ACSS2 and related genes, as well as CRISPR library screening and bioinformatics services.
Conclusion
Acetyl-CoA synthetase activity (GO:0003987) is a central metabolic function that links acetate utilization to acetyl-CoA production, histone acetylation, and lactylation. Its dysregulation contributes to cancer, kidney injury, neurodegeneration, and immune dysfunction. Understanding the molecular mechanism and regulatory networks of acetyl-CoA synthetase is essential for developing targeted therapies. EDITGENE provides comprehensive CRISPR cell model services to support mechanistic and translational research on this important enzyme activity.
References
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- 2. Mews P et al.. 2017. Acetyl-CoA synthetase regulates histone acetylation and hippocampal memory.. Nature 546(7658):381-386 PMID: 28562591
- 3. Schug ZT et al.. 2015. Acetyl-CoA synthetase 2 promotes acetate utilization and maintains cancer cell growth under metabolic stress.. Cancer Cell 27(1):57-71 PMID: 25584894
- 4. Lu J et al.. 2024. Acetyl-CoA synthetase 2 induces pyroptosis and inflammation of renal epithelial tubular cells in sepsis-induced acute kidney injury by upregulating the KLF5/NF-κB pathway.. Cell Commun Signal 22(1):187 PMID: 38515158
- 5. Lu J et al.. 2023. Activation of acetyl-CoA synthetase 2 mediates kidney injury in diabetic nephropathy.. JCI Insight 8(20) PMID: 37870960
- 6. Ma S et al.. 2025. Nutrient-driven histone code determines exhausted CD8(+) T cell fates.. Science 387(6734):eadj3020 PMID: 39666821
- 7. Wellen KE et al.. 2009. ATP-citrate lyase links cellular metabolism to histone acetylation.. Science 324(5930):1076-80 PMID: 19461003
- 8. Lin Y et al.. 2023. ACSS2-dependent histone acetylation improves cognition in mouse model of Alzheimer's disease.. Mol Neurodegener 18(1):47 PMID: 37438762
