GO:0071568 UFM1 transferase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0071568 (UFM1 transferase activity) catalyzes the covalent attachment of UFM1 to target proteins via an E1-E2-E3 enzymatic cascade.
• The UFM1 system is essential for DNA damage response, autophagy, ribosome quality control, and lipid metabolism.
• Key components include UBA5 (E1), UFC1 (E2), UFL1 (E3), and the UFM1-activating enzyme UBA5.
• Dysregulation of UFM1 transferase activity is implicated in cancer, atherosclerosis, and developmental disorders.
• CRISPR knockout, point mutation, and knock-in models are powerful tools to dissect UFM1 transferase function in human cells.
• EDITGENE provides comprehensive CRISPR services to study UFM1 transferase activity and its downstream effects.
Description
UFM1 transferase activity (GO:0071568) is a molecular function that catalyzes the transfer of ubiquitin-fold modifier 1 (UFM1) from a UFM1-conjugated protein to a target protein, forming a covalent linkage. This process, known as UFMylation, is a post-translational modification analogous to ubiquitination but distinct in its enzymatic machinery and substrate specificity. The reaction proceeds via a three-step cascade involving UBA5 (E1 activating enzyme), UFC1 (E2 conjugating enzyme), and UFL1 (E3 ligase), which together mediate the attachment of UFM1 to lysine residues on substrate proteins. UFM1 transferase activity is critical for diverse cellular processes, including the DNA damage response, autophagy, endoplasmic reticulum stress, and lipid metabolism. Researchers study this activity to understand its roles in development, homeostasis, and disease, and to identify therapeutic targets for cancer, neurodegeneration, and metabolic disorders.
UFM1 transferase activity At A Glance
| GO ID | GO:0071568 |
|---|---|
| GO term | UFM1 transferase activity |
| Ontology | molecular_function |
| Synonym | None |
| Major function | Catalyzes covalent attachment of UFM1 to target proteins |
| Enzymatic components | UBA5 (E1), UFC1 (E2), UFL1 (E3) |
| Substrate | UFM1-conjugated proteins and target lysine residues |
| Reaction | X-UFM1 + Y = Y-UFM1 + X |
What Is GO:0071568?
UFM1 transferase activity is defined as the catalysis of UFM1 transfer from one protein to another via the reaction X-UFM1 + Y = Y-UFM1 + X, where both X-UFM1 and Y-UFM1 are covalent linkages. In simpler terms, it is the enzymatic activity that attaches the small protein UFM1 to target proteins, similar to how ubiquitin is attached, but using a dedicated set of enzymes.
Why Is UFM1 transferase activity Important in Cell Biology?
UFM1 transferase activity is essential for maintaining cellular homeostasis and responding to stress. It regulates key pathways such as the DNA damage response, where UFMylation of MRE11 and histone H4 promotes ATM activation. It also controls autophagy initiation by stabilizing BECN1, and modulates lipid transport in intestinal enterocytes. Dysregulation of UFM1 transferase activity has been linked to cancer progression, atherosclerosis, and developmental defects, making it a promising target for therapeutic intervention.
• Regulates DNA damage response and genome stability through ATM activation.
• Controls autophagy initiation by stabilizing BECN1.
• Modulates ribosomal DNA-damage response and ribosome quality control.
• Influences lipid metabolism and systemic lipid balance.
• Suppresses invasive activities of gastric cancer cells.
• Attenuates atherosclerosis by inhibiting VSMC phenotypic switching.
• Essential for embryonic development and cellular stress responses.
• Provides a potential therapeutic target for cancer and metabolic diseases.
What Happens During UFM1 transferase activity?
Activation of UFM1 by UBA5
In simple terms: UFM1 is first activated by the E1 enzyme UBA5 in an ATP-dependent manner.
The UFM1 transferase cascade begins with the activation of UFM1 by UBA5, the E1 activating enzyme. UBA5 forms a thioester bond with UFM1 in an ATP-dependent reaction, preparing UFM1 for transfer to the E2 enzyme.
Conjugation to UFC1
In simple terms: Activated UFM1 is transferred to the E2 enzyme UFC1.
The activated UFM1 is then transferred from UBA5 to the E2 conjugating enzyme UFC1, forming a UFM1-UFC1 thioester intermediate. This step is essential for subsequent transfer to the target protein.
Ligation to target proteins by UFL1
In simple terms: The E3 ligase UFL1 attaches UFM1 to specific target proteins.
UFL1, the E3 ligase, facilitates the transfer of UFM1 from UFC1 to a lysine residue on the target protein, forming a covalent isopeptide bond. This step determines substrate specificity and is regulated by additional factors such as UFBP1 and CDK5RAP3.
Deconjugation by UFM1-specific proteases
In simple terms: UFM1 can be removed from target proteins by specific proteases.
UFM1-specific proteases, such as UFSP1 and UFSP2, can cleave UFM1 from target proteins, reversing the modification. This dynamic regulation is crucial for maintaining cellular homeostasis and preventing excessive UFMylation.
Key Genes Involved in GO:0071568 UFM1 transferase activity
The following genes and proteins are key components and regulators of UFM1 transferase activity.
| Gene | Major Role | Research Relevance |
|---|---|---|
| UFM1 | Ubiquitin-fold modifier 1; the modifier protein transferred | Central to all UFMylation studies |
| UBA5 | E1 activating enzyme for UFM1 | Initiates UFM1 transfer cascade |
| UFC1 | E2 conjugating enzyme for UFM1 | Mediates UFM1 transfer to E3 |
| UFL1 | E3 ligase for UFM1 | Determines substrate specificity |
| UFSP1 | UFM1-specific protease | Regulates UFM1 deconjugation |
| UFSP2 | UFM1-specific protease | Regulates UFM1 deconjugation |
| MRE11 | DNA damage response protein; UFMylation target | UFMylation promotes ATM activation |
| BECN1 | Autophagy initiator; UFMylation target | UFMylation stabilizes BECN1 |
| H4 | Histone H4; UFMylation target | UFMylation promotes ATM activation |
| ATM | DNA damage checkpoint kinase | Activated by UFMylation pathway |
| PDK1 | PI3K/AKT signaling kinase | UFM1 suppresses PDK1 expression |
| AKT | Serine/threonine kinase | UFM1 inhibits AKT phosphorylation |
| COPII | Vesicle coat complex | UFMylation-COPII axis regulates lipid transport |
| CDK5RAP3 | UFL1 adaptor protein | Regulates UFM1 transfer to substrates |
| UFBP1 | UFL1 adaptor protein | Regulates UFM1 transfer to substrates |
| VCP/p97 | AAA+ ATPase; UFMylation target | UFMylation stabilizes BECN1 |
How Is UFM1 transferase activity Regulated?
UFM1 transferase activity is regulated at multiple levels. The expression and activity of UBA5, UFC1, and UFL1 are modulated by cellular stress, including DNA damage and ER stress. UFM1-specific proteases (UFSP1/UFSP2) remove UFM1 from substrates, providing reversibility. Additionally, adaptor proteins such as UFBP1 and CDK5RAP3 enhance UFL1-mediated UFMylation of specific substrates. The pathway is also linked to AKT signaling, where UFM1 suppresses AKT phosphorylation.
UFM1 transferase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| UFM1 | Gastric cancer invasion | Knockout in gastric cancer cell lines |
| UFL1 | Atherosclerosis | VSMC-specific knockout mouse |
| UBA5 | DNA damage response defects | Knockout in HeLa or U2OS cells |
| UFC1 | Metabolic disorders | Intestinal enterocyte-specific knockout |
| UFSP2 | Developmental disorders | Patient-derived iPSCs |
UFM1 transferase activity in cancer
Dysregulation of UFM1 transferase activity has been observed in various cancers. In gastric cancer, UFM1 suppresses invasive activities by attenuating PDK1 expression through PI3K/AKT signaling. This suggests that loss of UFM1 transferase activity may promote tumor progression and metastasis.
UFM1 transferase activity in cardiovascular disease
UFM1 suppresses vascular smooth muscle cell phenotypic switching and attenuates atherosclerosis by inhibiting AKT phosphorylation. This indicates that UFM1 transferase activity plays a protective role in cardiovascular health.
UFM1 transferase activity in metabolic disorders
A UFMylation-COPII axis orchestrates lipid transport in intestinal enterocytes and regulates systemic lipid balance. Disruption of this axis may contribute to metabolic disorders such as dyslipidemia.
UFM1 transferase activity in DNA damage and genome stability
UFM1 transferase activity is essential for the DNA damage response. UFMylation of MRE11 and histone H4 promotes ATM activation, and loss of UFMylation leads to defective DNA repair and genome instability. This has implications for cancer predisposition and aging.
From UFM1 transferase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does UFM1 transferase activity regulate autophagy? | BECN1 knockout or UFM1 knockout cells |
| How does UFMylation affect DNA damage response? | MRE11 point mutant knock-in |
| What is the role of UFL1 in lipid transport? | Intestinal enterocyte-specific UFL1 knockout |
| Does UFM1 suppress cancer invasion? | UFM1 overexpression in gastric cancer cells |
| How does UFM1 affect atherosclerosis? | VSMC-specific UFM1 knockout mouse |
| What is the impact of UFM1 on ATM activation? | Histone H4 UFMylation site mutant knock-in |
How to Study the UFM1 transferase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| CRISPR knockout | Loss of gene function | Identify essential UFM1 pathway genes |
| Proteomics | UFMylome composition | Discover novel UFM1 substrates |
| Imaging | Subcellular localization | Track UFM1 conjugation in live cells |
| In vitro UFMylation assay | Enzymatic activity | Test inhibitors or mutations |
| RNA-seq | Transcriptional changes | Assess downstream effects of UFM1 loss |
| Ribo-seq | Translation efficiency | Measure impact on protein synthesis |
| Co-IP | Protein-protein interactions | Identify UFM1 machinery complexes |
CRISPR knockout screening
Genome-wide CRISPR knockout screens can identify genes required for UFM1 transferase activity and its downstream effects. For example, knockout of UBA5, UFC1, or UFL1 abolishes UFMylation and sensitizes cells to DNA damage.
Proteomics and UFMylome analysis
Mass spectrometry-based proteomics can map the UFMylome, identifying target proteins modified by UFM1. This approach has revealed substrates such as MRE11, BECN1, and histone H4.
Imaging and subcellular localization
Fluorescence microscopy can visualize UFM1 conjugation and localization of UFM1 machinery components. Tagged knock-in of UFM1 or UFL1 allows real-time tracking of UFMylation dynamics.
Biochemical assays for UFM1 transfer
In vitro UFMylation assays using recombinant UBA5, UFC1, UFL1, and UFM1 can measure transferase activity. These assays are useful for testing inhibitors or mutations.
How CRISPR Can Be Used to Study GO:0071568 UFM1 transferase activity
Knockout
CRISPR knockout of UFM1, UBA5, UFC1, or UFL1 completely abolishes UFM1 transferase activity, providing a clean background to study its cellular functions. For example, UFM1 knockout cells exhibit defective DNA damage response and autophagy.
Point Mutation
Point mutations in the catalytic residues of UBA5, UFC1, or UFL1 can selectively inactivate UFM1 transferase activity without affecting protein stability. Such models are useful to dissect the specific contribution of UFMylation to substrate modification.
Knock-in
Knock-in of tagged UFM1 (e.g., HA or GFP) allows endogenous tracking of UFM1 conjugation and identification of target proteins. Knock-in of UFMylation site mutants in substrates like MRE11 or histone H4 can reveal site-specific functions.
Overexpression
Overexpression of UFM1 or its enzymes can enhance UFMylation and suppress cancer cell invasion or atherosclerosis progression. Overexpression models are valuable for gain-of-function studies.
How EDITGENE Supports UFM1 transferase activity Research
Researchers studying UFM1 transferase activity-related genes often need to determine whether a candidate gene is causally involved in UFMylation, DNA damage response, autophagy, or disease progression. EDITGENE provides a comprehensive suite of CRISPR services to accelerate this research.
Contact EDITGENE today to design your custom CRISPR model for UFM1 transferase activity research.
Frequently Asked Questions About UFM1 transferase activity
What is UFM1 transferase activity?
UFM1 transferase activity (GO:0071568) is the enzymatic activity that catalyzes the covalent attachment of UFM1 to target proteins via an E1-E2-E3 cascade.
What genes are involved in UFM1 transferase activity?
Key genes include UFM1, UBA5 (E1), UFC1 (E2), UFL1 (E3), and the proteases UFSP1/UFSP2.
What is the role of UFM1 transferase activity in DNA damage response?
It promotes ATM activation through UFMylation of MRE11 and histone H4, facilitating DNA repair.
How is UFM1 transferase activity linked to cancer?
UFM1 suppresses gastric cancer invasion by attenuating PDK1 expression through PI3K/AKT signaling.
What diseases are associated with UFM1 transferase activity?
Dysregulation is linked to cancer, atherosclerosis, metabolic disorders, and developmental defects.
What are the main enzymes in UFM1 transferase activity?
UBA5 (E1), UFC1 (E2), and UFL1 (E3) are the core enzymes.
How can I study UFM1 transferase activity using CRISPR?
CRISPR knockout, point mutation, knock-in, and overexpression models can be used to dissect its functions.
What is the difference between UFMylation and ubiquitination?
UFMylation uses UFM1 and a dedicated E1-E2-E3 cascade (UBA5, UFC1, UFL1), while ubiquitination uses ubiquitin and different enzymes.
What are the substrates of UFM1 transferase activity?
Known substrates include MRE11, BECN1, histone H4, and VCP/p97.
How does UFM1 transferase activity regulate autophagy?
UFMylation stabilizes BECN1, facilitating the initiation of autophagy.
Conclusion
UFM1 transferase activity (GO:0071568) is a critical post-translational modification system that regulates DNA damage response, autophagy, lipid metabolism, and disease progression. Its core enzymes UBA5, UFC1, and UFL1 are attractive targets for therapeutic intervention. CRISPR-based models are indispensable for dissecting the molecular mechanisms and disease relevance of UFM1 transferase activity. EDITGENE offers comprehensive CRISPR services to support your research in this field.
References
- 1. Wang Z et al.. 2024. VCP/p97 UFMylation stabilizes BECN1 and facilitates the initiation of autophagy.. Autophagy 20(9):2041-2054 PMID: 38762759
- 2. Wang Z et al.. 2019. MRE11 UFMylation promotes ATM activation.. Nucleic Acids Res 47(8):4124-4135 PMID: 30783677
- 3. Panichnantakul P et al.. 2024. Protein UFMylation regulates early events during ribosomal DNA-damage response.. Cell Rep 43(9):114738 PMID: 39277864
- 4. Lin JX et al.. 2019. UFM1 suppresses invasive activities of gastric cancer cells by attenuating the expres7sion of PDK1 through PI3K/AKT signaling.. J Exp Clin Cancer Res 38(1):410 PMID: 31533855
- 5. Wang Y et al.. 2026. A UFMylation-COPII axis orchestrates lipid transport in intestinal enterocytes and regulates systemic lipid balance.. Mol Metab 110:102397 PMID: 42285460
- 6. Zhang Q et al.. 2026. UFM1 suppresses VSMCs phenotypic switching and attenuates atherosclerosis by inhibiting AKT phosphorylation.. Biochem Pharmacol 250(Pt 1):117957 PMID: 41974329
- 7. Fang Z et al.. 2019. Essential Role of Ubiquitin-Fold Modifier 1 Conjugation in DNA Damage Response.. DNA Cell Biol 38(10):1030-1039 PMID: 31368785
- 8. Qin B et al.. 2019. UFL1 promotes histone H4 ufmylation and ATM activation.. Nat Commun 10(1):1242 PMID: 30886146
