GO:0050291 sphingosine N-acyltransferase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0050291 (sphingosine N-acyltransferase activity) catalyzes the reaction acyl-CoA + sphingosine = CoA + N-acylsphingosine, the terminal step of de novo ceramide biosynthesis.
• The enzymes responsible are the ceramide synthases (CerS1-CerS6 in mammals), each with distinct acyl-chain length preferences that determine the sphingolipid profile of a cell.
• Ceramide synthase activity is a central node in sphingolipid metabolism and is regulated by inflammatory cytokines such as IL-10, which constrains sphingolipid metabolism to limit inflammation.
• Dysregulated ceramide synthase activity is implicated in colorectal cancer, diabetic kidney disease, aortic aneurysm, and tumor suppression via mitophagy.
• Microbial metabolites and bile acids can modulate ceramide synthase activity, linking the microbiome to host sphingolipid homeostasis.
• CRISPR knockout, point-mutation, knock-in, and overexpression models are essential for dissecting the causal roles of individual CerS isoforms in health and disease.
Description
Sphingosine N-acyltransferase activity (GO:0050291) is a molecular function that catalyzes the formation of N-acylsphingosine (ceramide) from sphingosine and an acyl-CoA donor. This reaction is the final step in the de novo sphingolipid biosynthesis pathway and is also part of the salvage pathway that recycles sphingosine back to ceramide. The enzymes that carry out this activity are known as ceramide synthases (CerS), and in mammals there are six isoforms (CerS1-CerS6), each exhibiting distinct acyl-CoA chain-length specificity. Because ceramides are bioactive lipids that regulate membrane structure, inflammation, apoptosis, and metabolic stress, the activity of sphingosine N-acyltransferases is critical for cellular homeostasis. Researchers study this term to understand how specific ceramide species are generated and how their dysregulation contributes to diseases such as cancer, diabetes, and cardiovascular disorders. The availability of CRISPR-based tools now allows precise manipulation of CerS genes to establish causal links between this enzymatic activity and disease phenotypes.
sphingosine N-acyltransferase activity At A Glance
| GO ID | GO:0050291 |
|---|---|
| GO term | sphingosine N-acyltransferase activity |
| Ontology | molecular_function |
| Synonym | ceramide synthase activity; ceramide synthetase activity; dihydroceramide synthase activity; sphingosine acyltransferase activity; acyl-CoA:sphingosine N-acyltransferase activity |
| Major function | Catalysis of the reaction acyl-CoA + sphingosine = CoA + N-acylsphingosine, producing ceramide |
| Reaction direction | Acyl transfer from acyl-CoA to sphingosine base |
| Substrates | Sphingosine or dihydrosphingosine and various acyl-CoA species |
| Products | N-acylsphingosine (ceramide) or dihydroceramide and coenzyme A |
| Enzyme family | Ceramide synthases (CerS1-CerS6 in mammals) |
| Cellular location | Endoplasmic reticulum membrane |
| Pathway context | De novo sphingolipid biosynthesis and sphingosine salvage pathway |
What Is GO:0050291?
Sphingosine N-acyltransferase activity is defined by the Gene Ontology as the catalysis of the reaction: acyl-CoA + sphingosine = CoA + N-acylsphingosine. In this reaction, an acyl group from a fatty acyl-CoA is transferred to the amino group of sphingosine (or dihydrosphingosine), producing a ceramide (or dihydroceramide) and free coenzyme A. This activity is synonymous with ceramide synthase, ceramide synthetase, dihydroceramide synthase, and sphingosine acyltransferase activity. It is a molecular_function term that represents the enzymatic capability rather than a specific gene product, although in mammals it is primarily associated with the CerS family of enzymes.
Why Is sphingosine N-acyltransferase activity Important in Cell Biology?
Sphingosine N-acyltransferase activity is essential for the production of ceramides, which are not only structural components of cell membranes but also potent signaling molecules that regulate cell fate. The specific acyl chain length of ceramides influences their biological functions, and the ceramide synthase isoforms determine this specificity. Dysregulation of this activity has been linked to a wide range of pathologies, including cancer, inflammatory diseases, metabolic disorders, and cardiovascular conditions. Therefore, understanding the regulation and function of sphingosine N-acyltransferases is crucial for developing therapeutic strategies that target sphingolipid metabolism.
• Ceramide synthesis is a hub for sphingolipid metabolism, affecting membrane dynamics and signaling.
• Different CerS isoforms produce distinct ceramide species with unique roles in health and disease.
• IL-10 constrains sphingolipid metabolism by regulating ceramide synthase activity to limit inflammation.
• Microbial riboflavin inhibits CerS3, lowering ceramide (d18:1/26:0) and delaying colorectal cancer progression.
• CerS6 links ceramide metabolism to innate immune responses in diabetic kidney disease.
• Very long-chain fatty acids drive 1-deoxySphingolipid toxicity, implicating CerS in lipotoxicity.
• Ceramide-induced metabolic stress depletes fumarate and drives mitophagy to mediate tumor suppression.
• Ursodeoxycholic acid alleviates aortic aneurysm via the FXR/CerS2 axis, highlighting therapeutic potential.
• CerS2 and Tbc1D20 co-engineering improves secretory pathway in CHO producer cells.
• Mutations in bile acid CoA:N-acyltransferase alter activity and substrate specificity, providing insights into related acyltransferases.
What Happens During sphingosine N-acyltransferase activity?
Substrate recognition and binding
In simple terms: The enzyme grabs a sphingosine molecule and an acyl-CoA molecule to prepare them for joining.
The ceramide synthase enzyme binds sphingosine (or dihydrosphingosine) and an acyl-CoA of specific chain length. The active site accommodates the sphingoid base and the acyl-CoA thioester, positioning them for catalysis. Different CerS isoforms exhibit distinct acyl-CoA preferences, which determine the chain length of the resulting ceramide.
Catalytic acyl transfer
In simple terms: The acyl group is transferred from acyl-CoA to sphingosine, forming ceramide and releasing CoA.
The enzyme catalyzes the nucleophilic attack of the sphingosine amino group on the acyl-CoA thioester, resulting in the formation of an amide bond and release of coenzyme A. This reaction is the terminal step in de novo ceramide synthesis and also functions in the salvage pathway. The reaction is highly specific for the stereochemistry of sphingosine and the chain length of the acyl-CoA.
Product release and membrane integration
In simple terms: The newly made ceramide is released into the membrane where it can act as a signaling molecule.
After catalysis, the N-acylsphingosine (ceramide) product is released into the endoplasmic reticulum membrane, where it can be further metabolized to complex sphingolipids or act as a signaling lipid. Ceramide can also be transported to other organelles, such as mitochondria, to induce mitophagy and tumor suppression.
Regulation by inflammatory and metabolic signals
In simple terms: The activity of the enzyme can be turned up or down by signals like cytokines and metabolites.
IL-10 constrains sphingolipid metabolism by limiting the availability of substrates or by directly affecting ceramide synthase expression, thereby limiting inflammation. Microbial riboflavin inhibits CerS3, reducing specific ceramide species and delaying colorectal cancer progression. Ursodeoxycholic acid modulates the FXR/CerS2 axis to alleviate aortic aneurysm. These examples illustrate that sphingosine N-acyltransferase activity is dynamically regulated by external cues.
Key Genes Involved in GO:0050291 sphingosine N-acyltransferase activity
The following genes encode enzymes or regulators directly associated with sphingosine N-acyltransferase activity (GO:0050291).
| Gene | Major Role | Research Relevance |
|---|---|---|
| CERS1 | Ceramide synthase 1, preferentially uses C18:0 acyl-CoA | Expressed in brain; linked to neurodegeneration and myelin function |
| CERS2 | Ceramide synthase 2, synthesizes very long-chain ceramides | Role in secretory pathway, liver function, and aortic aneurysm |
| CERS3 | Ceramide synthase 3, produces ultra-long-chain ceramides | Inhibited by microbial riboflavin in colorectal cancer |
| CERS4 | Ceramide synthase 4, uses C18:0 and C20:0 acyl-CoA | Less studied; potential role in skin and barrier function |
| CERS5 | Ceramide synthase 5, synthesizes C16:0 ceramides | Implicated in metabolic stress and apoptosis |
| CERS6 | Ceramide synthase 6, produces C16:0 ceramides | Links ceramide metabolism to innate immunity in diabetic kidney disease |
| IL10 | Anti-inflammatory cytokine that constrains sphingolipid metabolism | Regulates ceramide synthase activity to limit inflammation |
| FXR | Nuclear receptor regulating bile acid and lipid metabolism | Modulates CerS2 axis in aortic aneurysm |
| TBC1D20 | Rab GTPase-activating protein involved in secretory pathway | Co-engineered with CerS2 to improve CHO cell secretion |
| BAAT | Bile acid CoA:N-acyltransferase, related acyltransferase | Mutations alter activity and substrate specificity |
| SPTLC1 | Serine palmitoyltransferase subunit 1, upstream of ceramide synthesis | Provides substrates for ceramide synthases |
| SPTLC2 | Serine palmitoyltransferase subunit 2 | Upstream enzyme in sphingolipid biosynthesis |
| DEGS1 | Dihydroceramide desaturase, converts dihydroceramide to ceramide | Works downstream of ceramide synthase |
| ACER1 | Alkaline ceramidase 1, hydrolyzes ceramide to sphingosine | Recycles sphingosine for salvage pathway |
| ACER2 | Alkaline ceramidase 2 | Regulates sphingosine levels for ceramide synthase |
| ACER3 | Alkaline ceramidase 3 | Affects ceramide/sphingosine balance |
| SGMS1 | Sphingomyelin synthase 1, uses ceramide as substrate | Downstream of ceramide synthase |
| SGMS2 | Sphingomyelin synthase 2 | Downstream of ceramide synthase |
How Is sphingosine N-acyltransferase activity Regulated?
Sphingosine N-acyltransferase activity is regulated at multiple levels. Transcriptional regulation of CerS genes occurs in response to inflammatory cytokines such as IL-10, which constrains sphingolipid metabolism to limit inflammation. Post-translational modifications and protein-protein interactions also modulate enzyme activity. Metabolites such as microbial riboflavin can directly inhibit specific CerS isoforms, as shown for CerS3 in colorectal cancer. Bile acids and nuclear receptors like FXR influence CerS2 expression in cardiovascular contexts. Additionally, substrate availability (sphingosine and acyl-CoA) and product feedback likely play roles in fine-tuning activity.
sphingosine N-acyltransferase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| CERS3 | Colorectal cancer | KO and overexpression in HCT116 or SW480 cells |
| CERS6 | Diabetic kidney disease | KO mice or podocyte-specific KO |
| CERS2 | Aortic aneurysm and dissection | Intestinal-specific KO or overexpression |
| CERS1 | Neurodegeneration | Neuron-specific KO or knock-in |
| CERS5 | Tumor suppression via mitophagy | Cancer cell lines with KO and point mutations |
Cancer
Ceramide synthase activity is frequently dysregulated in cancer. Microbial riboflavin inhibits CerS3, lowering ceramide (d18:1/26:0) and delaying colorectal cancer progression. Ceramide-induced metabolic stress depletes fumarate and drives mitophagy to mediate tumor suppression, highlighting the role of ceramide synthases in cancer cell death. These findings suggest that modulating sphingosine N-acyltransferase activity could be a therapeutic strategy.
Metabolic and kidney diseases
CerS6 links ceramide metabolism to innate immune responses in diabetic kidney disease, indicating that specific ceramide species contribute to renal inflammation and injury. Very long-chain fatty acids drive 1-deoxySphingolipid toxicity, which may involve ceramide synthase activity and contribute to metabolic stress.
Cardiovascular disease
Ursodeoxycholic acid alleviates aortic aneurysm and dissection through the intestinal farnesoid X receptor/ceramide synthase 2 axis, demonstrating that CerS2 activity in the gut-liver axis influences vascular pathology. This highlights the systemic impact of sphingosine N-acyltransferase activity.
Inflammation
IL-10 constrains sphingolipid metabolism to limit inflammation, directly implicating ceramide synthase activity in the resolution of inflammatory responses. Dysregulation of this pathway may contribute to chronic inflammatory diseases.
From sphingosine N-acyltransferase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of CerS3 reduce specific ceramides and affect cancer growth? | CERS3 knockout in colorectal cancer cell lines |
| Does CerS6 mediate innate immune responses in diabetic kidney disease? | CERS6 knockout mice or kidney-specific KO |
| Can point mutations in CerS alter acyl-chain specificity? | CRISPR point mutation knock-in of catalytic residues |
| Does overexpression of CerS2 improve secretory pathway? | CERS2 overexpression in CHO cells |
| Does CerS1 deficiency cause neurodegeneration? | CERS1 knockout neurons or mouse models |
| Does FXR regulate CerS2 in aortic aneurysm? | FXR knockout or intestinal-specific overexpression |
How to Study the sphingosine N-acyltransferase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| LC-MS lipidomics | Ceramide species and chain lengths | Quantify changes in sphingolipid profile after CerS manipulation |
| Radioactive enzyme assay | Ceramide synthase activity | Measure kinetic parameters and substrate specificity |
| CRISPR knockout screen | Genes affecting ceramide levels | Identify modifiers of sphingolipid metabolism |
| RNA-seq | Transcript levels of CerS and related genes | Assess regulation by cytokines or metabolites |
| Western blot | Protein expression of CerS isoforms | Validate knockout or overexpression |
| Immunofluorescence | Subcellular localization of CerS | Determine ER localization and trafficking |
| Mitophagy assay | Ceramide-induced mitophagy | Study tumor suppression mechanisms |
| Acyl-CoA profiling | Substrate availability | Link metabolic state to ceramide synthesis |
Lipidomics and mass spectrometry
Mass spectrometry-based lipidomics is the primary method to measure ceramide species produced by sphingosine N-acyltransferase activity. It can quantify chain-length-specific ceramides and assess the impact of genetic or pharmacological perturbations.
Enzymatic activity assays
In vitro assays using fluorescent or radioactive acyl-CoA and sphingosine can directly measure ceramide synthase activity. These assays are useful for determining kinetic parameters and substrate specificity of different CerS isoforms.
CRISPR screening and functional genomics
CRISPR knockout screens can identify genes that modulate ceramide levels or sensitivity to ceramide-induced cell death. Such screens have revealed roles for CerS isoforms in cancer and metabolic diseases.
Transcriptomics and proteomics
RNA-seq and proteomics can assess expression changes in CerS genes and related pathway components under various conditions, such as inflammation or metabolic stress.
How CRISPR Can Be Used to Study GO:0050291 sphingosine N-acyltransferase activity
Knockout
CRISPR knockout of individual CERS genes allows researchers to determine the specific contribution of each isoform to total sphingosine N-acyltransferase activity and to disease phenotypes. For example, CERS3 knockout in colorectal cancer cells reduces specific ceramide species and affects tumor progression. CERS6 knockout in mice reveals its role in diabetic kidney disease.
Point Mutation
Point mutations can be introduced into the catalytic domain of CerS enzymes to dissect substrate specificity and catalytic mechanism. For instance, mutations in bile acid CoA:N-acyltransferase alter activity and substrate specificity, providing a template for similar studies on CerS.
Knock-in
Knock-in of tagged or reporter versions of CerS genes enables visualization and purification of the enzyme complexes. This approach can reveal dynamic localization and interaction partners in live cells.
Overexpression
Overexpression of specific CerS isoforms in cell lines or animal models can drive production of particular ceramide species and test their downstream effects. For example, CERS2 overexpression in CHO cells improves secretory pathway function.
How EDITGENE Supports sphingosine N-acyltransferase activity Research
Researchers studying sphingosine N-acyltransferase activity-related genes often need to determine whether a candidate gene is causally involved in ceramide synthesis, disease progression, or therapeutic response. Establishing causality requires precise genetic manipulation, which is best achieved with CRISPR-based models.
Contact EDITGENE today to design your custom CRISPR model for sphingosine N-acyltransferase activity research.
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| CERS2 Knockout HEK293 Cell Line | EDJ-KQ1732 | Human | 29956 | Details Get a Quote |
| CERS4 Knockout HEK293 Cell Line | EDJ-KQ1733 | Human | 79603 | Details Get a Quote |
| CERS3 Knockout HEK293 Cell Line | EDJ-KQ1735 | Human | 204219 | Details Get a Quote |
| CERS6 Knockout HEK293 Cell Line | EDJ-KQ1736 | Human | 253782 | Details Get a Quote |
| CERS5 Knockout HEK293 Cell Line | EDJ-KQ1737 | Human | 91012 | Details Get a Quote |
| TLCD3B Knockout HEK293 Cell Line | EDJ-KQ9895 | Human | 83723 | Details Get a Quote |
| CERS4 Knockout HCT 116 Cell Line | EDJ-KQ20231 | Human | 79603 | Details Get a Quote |
| CERS2 Knockout A-549 Cell Line | EDJ-KQ21576 | Human | 29956 | Details Get a Quote |
| CERS2 Knockout HCT 116 Cell Line | EDJ-KQ21577 | Human | 29956 | Details Get a Quote |
| CERS2 Knockout HeLa Cell Line | EDJ-KQ21578 | Human | 29956 | Details Get a Quote |
| CERS4 Knockout A-549 Cell Line | EDJ-KQ21579 | Human | 79603 | Details Get a Quote |
| CERS6 Knockout A-549 Cell Line | EDJ-KQ21580 | Human | 253782 | Details Get a Quote |
| CERS6 Knockout HCT 116 Cell Line | EDJ-KQ21581 | Human | 253782 | Details Get a Quote |
| CERS6 Knockout HeLa Cell Line | EDJ-KQ21582 | Human | 253782 | Details Get a Quote |
| CERS5 Knockout A-549 Cell Line | EDJ-KQ21583 | Human | 91012 | Details Get a Quote |
Displaying Records 1 To 15 Of 28 Records
Frequently Asked Questions About sphingosine N-acyltransferase activity
What is sphingosine N-acyltransferase activity?
It is the enzymatic activity that catalyzes the reaction acyl-CoA + sphingosine = CoA + N-acylsphingosine, producing ceramide. It is classified as GO:0050291.
What genes are involved in sphingosine N-acyltransferase activity?
The main genes are CERS1 through CERS6, which encode ceramide synthases with different acyl-chain specificities.
What is the role of ceramide synthase in cancer?
Ceramide synthases can influence cancer progression. For example, inhibition of CerS3 by microbial riboflavin delays colorectal cancer progression, and ceramide-induced mitophagy mediates tumor suppression.
How is sphingosine N-acyltransferase activity regulated?
It is regulated by inflammatory cytokines like IL-10, microbial metabolites, bile acids via FXR, and substrate availability.
What diseases are associated with ceramide synthase dysfunction?
Dysfunction is linked to colorectal cancer, diabetic kidney disease, aortic aneurysm, neurodegeneration, and inflammatory disorders.
What are the synonyms for GO:0050291?
Synonyms include ceramide synthase activity, ceramide synthetase activity, dihydroceramide synthase activity, and sphingosine acyltransferase activity.
Which CerS isoform produces C16:0 ceramide?
CerS5 and CerS6 preferentially synthesize C16:0 ceramides.
How can I study sphingosine N-acyltransferase activity in the lab?
Common methods include lipidomics, enzymatic assays, CRISPR knockout, and overexpression models.
What is the cellular location of sphingosine N-acyltransferase activity?
The enzymes are located in the endoplasmic reticulum membrane.
Can CRISPR be used to model ceramide synthase mutations?
Yes, CRISPR knockout, point mutation, and knock-in models are powerful tools to study CerS function and disease-associated variants.
Conclusion
Sphingosine N-acyltransferase activity (GO:0050291) is a fundamental enzymatic activity in sphingolipid metabolism, responsible for ceramide synthesis. Its dysregulation is implicated in cancer, metabolic diseases, and cardiovascular disorders. The six ceramide synthase isoforms provide specificity and regulatory complexity, making them attractive targets for therapeutic intervention. Advances in CRISPR-based genome editing and lipidomics now enable precise dissection of this activity in health and disease, offering new opportunities for drug discovery and personalized medicine.
References
- 1. York AG et al.. 2024. IL-10 constrains sphingolipid metabolism to limit inflammation.. Nature 627(8004):628-635 PMID: 38383790
- 2. Qu R et al.. 2025. Microbial riboflavin inhibits ceramide synthase 3 to lower ceramide (d18:1/26:0) and delay colorectal cancer progression.. Cell Metab 37(9):1852-1869.e8 PMID: 40609532
- 3. Zhu Z et al.. 2025. CerS6 links ceramide metabolism to innate immune responses in diabetic kidney disease.. Nat Commun 16(1):1528 PMID: 39934147
- 4. Majcher A et al.. 2025. Very long-chain fatty acids drive 1-deoxySphingolipid toxicity.. Nat Commun 16(1):11650 PMID: 41298489
- 5. Oleinik NV et al.. 2025. Ceramide-Induced Metabolic Stress Depletes Fumarate and Drives Mitophagy to Mediate Tumor Suppression.. Cancer Res 85(17):3313-3334 PMID: 40540357
- 6. Pieper LA et al.. 2017. Secretory pathway optimization of CHO producer cells by co-engineering of the mitosRNA-1978 target genes CerS2 and Tbc1D20.. Metab Eng 40:69-79 PMID: 28088541
- 7. Styles NA et al.. 2016. Carboxy-terminal mutations of bile acid CoA:N-acyltransferase alter activity and substrate specificity.. J Lipid Res 57(7):1133-43 PMID: 27230263
- 8. Zhang Z et al.. 2025. Ursodeoxycholic acid alleviates aortic aneurysm and dissection through the intestinal farnesoid X receptor/ceramide synthase 2 axis.. Commun Biol 8(1):1009 PMID: 40617906
