GO:0035338 long-chain fatty-acyl-CoA biosynthetic process: Pathway, Genes, Functions and Research Methods

Research-grade guide for scientists and biopharma professionals

Key Takeaways

GO:0035338 describes the biosynthesis of long-chain fatty-acyl-CoA esters, which are essential intermediates in fatty acid metabolism and lipid synthesis.
Long-chain fatty-acyl-CoA synthetases (ACSLs) activate fatty acids by ligating them to coenzyme A, a reaction that requires ATP and produces AMP and pyrophosphate.
These molecules are not only metabolic intermediates but also signaling molecules that regulate AMPK, insulin sensitivity, and gene expression.
Dysregulation of long-chain fatty-acyl-CoA biosynthesis is linked to metabolic diseases such as nonalcoholic fatty liver disease, insulin resistance, and cancer.
Key enzymes include ACSL family members (ACSL1, ACSL3, ACSL4, ACSL5, ACSL6) and fatty acid transport proteins.
CRISPR-based models (knockout, knock-in, overexpression) are powerful tools to dissect the causal roles of genes in this pathway.

Description

Long-chain fatty-acyl-CoA biosynthetic process (GO:0035338) is a fundamental metabolic pathway that converts long-chain fatty acids into their activated coenzyme A (CoA) thioesters. This process is essential for channeling fatty acids into diverse metabolic fates, including beta-oxidation for energy production, phospholipid synthesis for membrane biogenesis, and protein acylation for signaling. The activation step is catalyzed by long-chain fatty-acyl-CoA synthetases (ACSLs), which couple fatty acid with CoA in an ATP-dependent manner. Beyond their role as metabolic intermediates, long-chain fatty-acyl-CoA esters act as signaling molecules that modulate cellular processes such as insulin sensitivity, AMPK activation, and gene expression. Consequently, understanding the regulation and function of this pathway is critical for deciphering mechanisms of metabolic diseases, including obesity, type 2 diabetes, nonalcoholic fatty liver disease, and cancer. Researchers studying this process rely on a combination of biochemical assays, genetic models, and advanced omics technologies to uncover its complexities.

long-chain fatty-acyl-CoA biosynthetic process At A Glance

GO ID GO:0035338
GO term long-chain fatty-acyl-CoA biosynthetic process
Ontology biological_process
Synonym None
Major function Activation of long-chain fatty acids by conjugation to coenzyme A, enabling their participation in energy metabolism, lipid synthesis, and signaling.
Key enzymes Long-chain fatty-acyl-CoA synthetases (ACSL1, ACSL3, ACSL4, ACSL5, ACSL6).
Substrates Long-chain fatty acids (C14-C24), ATP, coenzyme A.
Products Long-chain fatty-acyl-CoA, AMP, pyrophosphate.
Cellular locations Cytosol, mitochondria, peroxisomes, endoplasmic reticulum.
Related pathways Fatty acid beta-oxidation, phospholipid biosynthesis, protein acylation.

What Is GO:0035338?

The long-chain fatty-acyl-CoA biosynthetic process (GO:0035338) refers to the chemical reactions and pathways resulting in the formation of long-chain fatty-acyl-CoA molecules, which are fatty acids of chain length C14 to C24 covalently linked to coenzyme A via a thioester bond. This process is primarily catalyzed by the ACSL family of enzymes and is a prerequisite for both fatty acid degradation and lipid biosynthesis.

Why Is long-chain fatty-acyl-CoA biosynthetic process Important in Cell Biology?

The long-chain fatty-acyl-CoA biosynthetic process is a central hub in lipid metabolism, controlling the flux of fatty acids into catabolic and anabolic pathways. It is indispensable for energy homeostasis, membrane biogenesis, and the production of lipid signaling molecules. Dysregulation of this process contributes to the pathogenesis of prevalent metabolic disorders, including insulin resistance, nonalcoholic fatty liver disease, and certain cancers. Moreover, long-chain fatty-acyl-CoA esters serve as critical sensors of cellular energy status, directly influencing AMPK activity and gene expression programs. Therefore, studying this pathway offers insights into fundamental biology and provides potential therapeutic targets for metabolic diseases.
Essential for fatty acid beta-oxidation and energy production.
Required for phospholipid and triacylglycerol synthesis.
Provides substrates for protein acylation, affecting protein localization and function.
Regulates AMPK signaling and cellular energy sensing.
Implicated in insulin resistance in skeletal muscle.
Linked to nonalcoholic fatty liver disease progression.
Plays a role in cancer cell metabolism and proliferation.
Target for pharmacological interventions (e.g., etomoxir).
Involved in macrophage polarization and inflammation.
Key to understanding metabolic reprogramming in various diseases.

What Happens During long-chain fatty-acyl-CoA biosynthetic process?

Fatty Acid Uptake and Activation
In simple terms: Fatty acids enter the cell and are primed for use by attaching to a carrier molecule.
Long-chain fatty acids are transported across the plasma membrane by fatty acid transport proteins (FATPs) and CD36. Once inside, they are activated by ACSL enzymes, which catalyze the ATP-dependent ligation of the fatty acid to coenzyme A, forming long-chain fatty-acyl-CoA. This reaction proceeds via a two-step mechanism: first, the fatty acid reacts with ATP to form an acyl-AMP intermediate, releasing pyrophosphate; second, the acyl group is transferred to CoA, releasing AMP.
Subcellular Compartmentalization
In simple terms: Different parts of the cell handle distinct pools of activated fatty acids.
ACSL enzymes are localized to various organelles, including the endoplasmic reticulum, mitochondria, and peroxisomes. This compartmentalization directs fatty-acyl-CoAs toward specific metabolic fates: mitochondrial ACSL1 channels fatty acids into beta-oxidation, while ER-localized ACSL3 and ACSL4 support lipid synthesis. The acyl-CoA pool is also influenced by acyl-CoA binding proteins (ACBPs) that buffer and transport these hydrophobic molecules.
Metabolic Fates of Long-Chain Fatty-Acyl-CoA
In simple terms: Activated fatty acids can be burned for energy or used as building blocks.
Long-chain fatty-acyl-CoAs are partitioned into catabolic and anabolic pathways. In mitochondria, they undergo beta-oxidation to generate acetyl-CoA, which enters the TCA cycle to produce ATP. In the cytosol and ER, they serve as substrates for glycerolipid synthesis, including phospholipids and triacylglycerols. Additionally, they can be used for protein acylation, such as palmitoylation, which regulates protein trafficking and signaling.
Signaling Functions of Long-Chain Fatty-Acyl-CoA
In simple terms: These molecules also act as signals that tell the cell about its energy status.
Beyond metabolism, long-chain fatty-acyl-CoAs modulate signaling pathways. They activate AMPK by promoting its phosphorylation, thereby inhibiting anabolic processes and stimulating catabolism. They also influence insulin sensitivity; elevated levels of long-chain fatty-acyl-CoA in skeletal muscle are associated with insulin resistance. Furthermore, they can regulate gene expression by acting as ligands for nuclear receptors and by affecting protein acetylation.

Key Genes Involved in GO:0035338 long-chain fatty-acyl-CoA biosynthetic process

The following genes encode enzymes, transporters, and regulatory proteins that directly participate in or regulate the long-chain fatty-acyl-CoA biosynthetic process.
GeneMajor RoleResearch Relevance
ACSL1 Converts long-chain fatty acids to acyl-CoA; predominant in liver, adipose, heart Key for beta-oxidation and lipid synthesis; knockout models show impaired fatty acid oxidation.
ACSL3 Activates fatty acids for lipid synthesis; localized to ER and lipid droplets Involved in lipogenesis and cancer; knockdown reduces proliferation.
ACSL4 Activates arachidonic acid and other PUFAs; ER localization Linked to ferroptosis and cancer; knockout sensitizes to ferroptosis.
ACSL5 Activates fatty acids in liver and intestine; regulated by SIRT6 Deacetylation by SIRT6 enhances activity, promoting fatty acid oxidation and impeding NAFLD.
ACSL6 Activates long-chain fatty acids in brain and testis Potential role in neurological disorders; knockout affects lipid metabolism.
SLC27A1 (FATP1) Fatty acid transport protein; facilitates uptake of long-chain fatty acids Overexpression increases fatty acid uptake and acyl-CoA synthesis.
SLC27A2 (FATP2) Fatty acid transport and activation; very long-chain acyl-CoA synthetase Mutations cause metabolic disorders; knockout alters lipid profiles.
CD36 Fatty acid translocase; mediates uptake of long-chain fatty acids Deficiency reduces fatty acid uptake and acyl-CoA levels.
ACBP (DBI) Acyl-CoA binding protein; buffers and transports acyl-CoAs Modulates acyl-CoA availability for enzymes and signaling.
CPT1A Carnitine palmitoyltransferase 1A; converts acyl-CoA to acylcarnitine for mitochondrial import Rate-limiting for beta-oxidation; inhibited by malonyl-CoA.
SIRT6 Deacetylates ACSL5, enhancing its activity Links NAD+ metabolism to fatty acid oxidation; protective against NAFLD.
AMPK Energy sensor; activated by long-chain acyl-CoAs Mediates metabolic adaptations to energy stress.
PPARα Nuclear receptor; activated by fatty acids and acyl-CoAs Regulates genes involved in fatty acid oxidation.
SREBP1c Transcription factor; promotes lipogenic gene expression Increases ACSL and FASN expression, boosting acyl-CoA synthesis.
ACC1 Acetyl-CoA carboxylase; produces malonyl-CoA, a precursor for fatty acid synthesis Malonyl-CoA inhibits CPT1A, linking synthesis and oxidation.
FASN Fatty acid synthase; synthesizes long-chain fatty acids Provides substrates for ACSL-mediated activation.
SCD1 Stearoyl-CoA desaturase; introduces double bonds into fatty acids Modifies acyl-CoA composition; knockout alters lipid metabolism.
ELOVL6 Elongase; elongates fatty acids to long-chain Knockout affects acyl-CoA pool and insulin sensitivity.

How Is long-chain fatty-acyl-CoA biosynthetic process Regulated?

The long-chain fatty-acyl-CoA biosynthetic process is tightly regulated at multiple levels. Transcriptional control is mediated by lipogenic transcription factors such as SREBP1c and PPARα, which respond to nutritional and hormonal signals. Post-translational modifications, including acetylation and phosphorylation, modulate ACSL enzyme activity; for example, SIRT6-mediated deacetylation of ACSL5 enhances its catalytic activity and promotes fatty acid oxidation. Allosteric regulation by malonyl-CoA inhibits CPT1A, preventing futile cycling between fatty acid synthesis and oxidation. Additionally, AMPK senses long-chain acyl-CoA levels and phosphorylates downstream targets to maintain energy homeostasis. Hormones such as insulin and glucagon also influence the pathway by altering enzyme expression and activity.

long-chain fatty-acyl-CoA biosynthetic process and Human Disease

GeneDisease / BiologyPotential Experimental Model
ACSL5Nonalcoholic fatty liver disease (NAFLD)Liver-specific knockout or overexpression in mice; primary hepatocytes.
ACSL1Insulin resistance, cardiac dysfunctionSkeletal muscle-specific knockout; high-fat diet studies.
ACSL4Ferroptosis, cancerCancer cell lines with CRISPR knockout; xenograft models.
CPT1AInsulin resistance, metabolic syndromeEtomoxir treatment; liver-specific knockout.
SIRT6NAFLD, agingSIRT6 knockout mice; hepatocyte-specific overexpression.
Nonalcoholic Fatty Liver Disease (NAFLD)
Dysregulation of long-chain fatty-acyl-CoA biosynthesis contributes to hepatic steatosis and NAFLD. In a mouse model, cytoplasmic SIRT6 deacetylates ACSL5, increasing its activity and promoting fatty acid oxidation, thereby impeding NAFLD progression. Conversely, reduced ACSL5 activity leads to lipid accumulation and liver injury. These findings highlight the therapeutic potential of targeting ACSL5 and its regulators in NAFLD.
Insulin Resistance and Type 2 Diabetes
Elevated levels of long-chain fatty-acyl-CoA in skeletal muscle are associated with insulin resistance. Ruderman et al. proposed that accumulation of these metabolites contributes to impaired insulin signaling, possibly through activation of PKC isoforms and inhibition of IRS-1. This link underscores the importance of tightly regulating acyl-CoA synthesis and utilization to maintain glucose homeostasis.
Cancer Metabolism
Cancer cells often reprogram lipid metabolism to support rapid proliferation. ACSL enzymes, particularly ACSL3 and ACSL4, are upregulated in various cancers and contribute to oncogenic signaling and membrane synthesis. Etomoxir, an inhibitor of CPT1A, disrupts CoA homeostasis and has been shown to inhibit macrophage polarization, suggesting that targeting fatty-acyl-CoA metabolism may modulate the tumor microenvironment.
Neurological Disorders
In the brain, long-chain fatty-acyl-CoAs are essential for membrane lipid synthesis and protein acylation. Dysregulation of ACSL6, which is highly expressed in neurons, has been implicated in neurodevelopmental and neurodegenerative conditions, though the exact mechanisms remain under investigation.

From long-chain fatty-acyl-CoA biosynthetic process-Related Genes to Experimental Models

Research QuestionSuitable Model
Does ACSL5 loss affect hepatic lipid accumulation?ACSL5 knockout mice or CRISPR knockout in HepG2 cells.
How does ACSL1 contribute to muscle insulin sensitivity?Muscle-specific ACSL1 knockout mice; insulin tolerance tests.
What is the role of ACSL4 in ferroptosis?ACSL4 knockout cancer cell lines; lipid peroxidation assays.
Can SIRT6 deacetylation of ACSL5 be targeted to treat NAFLD?SIRT6 knockout mice with ACSL5 overexpression; pharmacological activators.
Does AMPK activation require long-chain acyl-CoA?AMPK knockout cells; acyl-CoA mimetics.
What is the impact of ACSL3 on cancer cell proliferation?ACSL3 knockdown or knockout in cancer cell lines; xenograft models.

How to Study the long-chain fatty-acyl-CoA biosynthetic process Process

MethodWhat It MeasuresTypical Application
ACSL activity assayEnzymatic conversion of fatty acid to acyl-CoAValidation of enzyme function; inhibitor screening.
CRISPR knockoutLoss-of-function phenotypeDetermining gene essentiality in metabolic pathways.
Metabolomics (LC-MS)Levels of acyl-CoA speciesProfiling metabolic changes in disease models.
LipidomicsComplex lipid compositionAssessing downstream effects on membrane lipids.
Western blotProtein expression and phosphorylationValidating knockout efficiency; signaling studies.
ImmunofluorescenceSubcellular localizationDetermining organelle-specific functions.
RNA-seqTranscriptional changesIdentifying compensatory gene expression.
Seahorse assayMitochondrial respiration and glycolysisMeasuring fatty acid oxidation capacity.
Biochemical Assays for ACSL Activity
ACSL enzyme activity can be measured using radiolabeled fatty acids (e.g., [14C]palmitate) and CoA, followed by extraction and separation of the acyl-CoA product by thin-layer chromatography or HPLC. Füllekrug et al. provide a detailed protocol for measuring long-chain fatty acyl-CoA synthetase activity in cell lysates or membrane fractions. This method is essential for validating enzyme function and screening inhibitors.
Genetic Knockout and Knockdown Models
CRISPR-Cas9 mediated knockout of ACSL genes in cell lines (e.g., HepG2, HEK293) allows researchers to assess loss-of-function phenotypes, such as changes in lipid accumulation, beta-oxidation rates, and signaling. Lentiviral shRNA knockdown provides a complementary approach for partial depletion. These models help establish causality between specific ACSL isoforms and metabolic outcomes.
Metabolomics and Lipidomics
Mass spectrometry-based metabolomics enables quantification of long-chain fatty-acyl-CoA species in cells and tissues. This approach can reveal how genetic or pharmacological perturbations alter the acyl-CoA pool and identify downstream metabolic changes. Lipidomics complements this by profiling complex lipids derived from acyl-CoAs.
Imaging and Subcellular Localization
Fluorescently tagged ACSL proteins (e.g., GFP-ACSL3) can be expressed in cells to visualize their subcellular localization using confocal microscopy. This helps determine whether enzymes localize to the ER, mitochondria, or lipid droplets, providing insight into their metabolic roles. Live-cell imaging can also track acyl-CoA dynamics using fluorescent biosensors.

How CRISPR Can Be Used to Study GO:0035338 long-chain fatty-acyl-CoA biosynthetic process

Knockout

CRISPR-Cas9 knockout of ACSL genes (e.g., ACSL1, ACSL5) in cell lines or animal models enables the study of loss-of-function phenotypes. For example, ACSL5 knockout in hepatocytes leads to reduced fatty acid oxidation and increased lipid accumulation, mimicking NAFLD features. Knockout models are also used to validate drug targets and assess metabolic flexibility.

Point Mutation

Introducing specific point mutations in ACSL genes (e.g., catalytic residues) via CRISPR base editing or homology-directed repair can dissect enzyme mechanism and identify residues critical for substrate binding or catalysis. Such models help distinguish between catalytic and non-catalytic functions of ACSL proteins.

Knock-in

Knock-in of tagged ACSL alleles (e.g., FLAG-ACSL5) allows for affinity purification and interactome analysis. Additionally, knock-in of disease-associated mutations (e.g., ACSL4 variants) can model human disorders in cell lines or mice, providing insights into genotype-phenotype relationships.

Overexpression

CRISPR activation (CRISPRa) or lentiviral overexpression of ACSL genes can elevate acyl-CoA levels and drive metabolic reprogramming. Overexpression of ACSL5 in hepatocytes enhances fatty acid oxidation and protects against steatosis, while ACSL3 overexpression promotes lipogenesis and cancer cell proliferation. These models are valuable for studying gain-of-function effects and identifying therapeutic targets.

How EDITGENE Supports long-chain fatty-acyl-CoA biosynthetic process Research

Researchers studying long-chain fatty-acyl-CoA biosynthetic process-related genes often need to determine whether a candidate gene is causally involved in metabolic phenotypes or disease progression. EDITGENE provides a comprehensive suite of CRISPR-based services to accelerate this discovery, from gene knockout to precise point mutations and overexpression models.
Contact EDITGENE today to design your custom CRISPR model for long-chain fatty-acyl-CoA biosynthetic process research.

Related Products

Product name Cat.No. Species Gene ID
ELOVL5 Knockout HEK293 Cell Line EDJ-KQ3092 Human 60481 Details Get a Quote
ELOVL4 Knockout HEK293 Cell Line EDJ-KQ3151 Human 6785 Details Get a Quote
HACD2 Knockout HEK293 Cell Line EDJ-KQ4909 Human 201562 Details Get a Quote
HACD1 Knockout HEK293 Cell Line EDJ-KQ6495 Human 9200 Details Get a Quote
ACSBG1 Knockout HEK293 Cell Line EDJ-KQ7883 Human 23205 Details Get a Quote
ACSL6 Knockout HEK293 Cell Line EDJ-KQ7951 Human 23305 Details Get a Quote
ACSBG2 Knockout HEK293 Cell Line EDJ-KQ9728 Human 81616 Details Get a Quote
ELOVL3 Knockout HEK293 Cell Line EDJ-KQ9839 Human 83401 Details Get a Quote
HSD17B12 Knockout HEK293 Cell Line EDJ-KQ10944 Human 51144 Details Get a Quote
ACSL5 Knockout HEK293 Cell Line EDJ-KQ11194 Human 51703 Details Get a Quote
ELOVL2 Knockout HEK293 Cell Line EDJ-KQ11923 Human 54898 Details Get a Quote
ACSF3 Knockout HEK293 Cell Line EDJ-KQ12263 Human 197322 Details Get a Quote
ACSL1 Knockout HEK293 Cell Line EDJ-KQ12265 Human 2180 Details Get a Quote
ACSL4 Knockout HEK293 Cell Line EDJ-KQ12266 Human 2182 Details Get a Quote
ELOVL1 Knockout HEK293 Cell Line EDJ-KQ13277 Human 64834 Details Get a Quote
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Frequently Asked Questions About long-chain fatty-acyl-CoA biosynthetic process

It is the metabolic pathway that activates long-chain fatty acids by attaching them to coenzyme A, forming long-chain fatty-acyl-CoA, which is essential for energy production and lipid synthesis.
Key genes include ACSL1, ACSL3, ACSL4, ACSL5, ACSL6, SLC27A1, SLC27A2, and CD36, which encode enzymes and transporters that facilitate fatty acid activation and uptake.
ACSL enzymes catalyze the ATP-dependent ligation of long-chain fatty acids to coenzyme A, producing fatty-acyl-CoA, a key intermediate in fatty acid metabolism.
It is regulated transcriptionally by SREBP1c and PPARα, post-translationally by acetylation (e.g., SIRT6 on ACSL5), and allosterically by malonyl-CoA and AMPK signaling.
Dysregulation is linked to nonalcoholic fatty liver disease, insulin resistance, type 2 diabetes, cancer, and neurological disorders.
Common methods include ACSL activity assays, CRISPR knockout models, metabolomics, and lipidomics to measure acyl-CoA levels and downstream effects.
SIRT6 deacetylates ACSL5, enhancing its activity and promoting fatty acid oxidation, which protects against nonalcoholic fatty liver disease.
Yes, elevated long-chain fatty-acyl-CoA in skeletal muscle is associated with insulin resistance, possibly through activation of PKC and impairment of insulin signaling.
Long-chain fatty-acyl-CoAs activate AMPK, a master energy sensor, leading to increased fatty acid oxidation and inhibited anabolic pathways.
Etomoxir inhibits CPT1A, blocking mitochondrial import of fatty-acyl-CoA and disrupting CoA homeostasis, which can affect macrophage polarization and cancer cell metabolism.

Conclusion

The long-chain fatty-acyl-CoA biosynthetic process (GO:0035338) is a cornerstone of lipid metabolism, integrating fatty acid activation with energy production, membrane synthesis, and signaling. Its dysregulation is implicated in prevalent metabolic diseases, making it a fertile ground for therapeutic discovery. Advances in CRISPR-based models and multi-omics technologies continue to unravel the complex regulation of this pathway, offering new opportunities for intervention. EDITGENE stands ready to support researchers with tailored CRISPR solutions to explore the roles of ACSL enzymes and related genes in health and disease.

References

  1. 1. Adeva-Andany MM et al.. 2019. Mitochondrial β-oxidation of saturated fatty acids in humans.. Mitochondrion 46:73-90 PMID: 29551309
  2. 3. Divakaruni AS et al.. 2018. Etomoxir Inhibits Macrophage Polarization by Disrupting CoA Homeostasis.. Cell Metab 28(3):490-503.e7 PMID: 30043752
  3. 4. Desjardins EM et al.. 2025. Sensing of Long-Chain Fatty Acyl-CoA Esters by AMPK.. Methods Mol Biol 2882:121-137 PMID: 39992507
  4. 5. Füllekrug J et al.. 2016. Measurement of Long-Chain Fatty Acyl-CoA Synthetase Activity.. Methods Mol Biol 1376:43-53 PMID: 26552674
  5. 6. Hou T et al.. 2022. Cytoplasmic SIRT6-mediated ACSL5 deacetylation impedes nonalcoholic fatty liver disease by facilitating hepatic fatty acid oxidation.. Mol Cell 82(21):4099-4115.e9 PMID: 36208627
  6. 7. Puthenveetil R et al.. 2022. Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases.. Curr Opin Struct Biol 77:102463 PMID: 36183446
  7. 8. Ruderman NB et al.. 1998. Malonyl CoA, long chain fatty acyl CoA and insulin resistance in skeletal muscle.. J Basic Clin Physiol Pharmacol 9(2-4):295-308 PMID: 10212840
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