GO:0035871 protein K11-linked deubiquitination: Mechanism, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0035871 describes the removal of K11-linked polyubiquitin chains from substrate proteins by deubiquitinating enzymes (DUBs).
• K11-linked chains are predominantly assembled by the anaphase-promoting complex/cyclosome (APC/C) with Ube2S and regulate cell cycle progression and protein stability.
• Cezanne (OTUD7B) is a key DUB that counteracts APC/C-mediated K11-linked ubiquitination to stabilize substrates such as BRCA1.
• USP38 removes K11-linked chains from HIF1α at Lys769 to enhance hypoxia signaling.
• Dysregulation of K11-linked deubiquitination is implicated in cancer, osteoarthritis, and coronavirus susceptibility.
• CRISPR knockout, point-mutation, knock-in, and overexpression models enable functional dissection of K11-linked deubiquitination in disease.
Description
Protein K11-linked deubiquitination (GO:0035871) is the biological process that removes polyubiquitin chains assembled through lysine 11 (K11) of ubiquitin from target proteins. This process is essential for reversing K11-linked ubiquitination, a modification primarily catalyzed by the anaphase-promoting complex/cyclosome (APC/C) together with the E2 enzyme Ube2S, which controls cell cycle progression and protein homeostasis. The discovery that Cezanne (OTUD7B) specifically disassembles K11-linked chains on BRCA1 highlighted the importance of this process in genome stability and tumor suppression. Beyond BRCA1, K11-linked deubiquitination regulates hypoxia signaling through HIF1α stabilization by USP38, and contributes to osteoarthritis pathogenesis via USP32-mediated PKM2 stabilization. Because K11-linked chains are distinct from other linkage types, their removal requires specialized DUBs with linkage specificity, making GO:0035871 a focal point for understanding how cells fine-tune protein stability in health and disease. Researchers study this process to identify therapeutic targets in cancer, metabolic disorders, and inflammatory conditions.
protein K11-linked deubiquitination At A Glance
| GO ID | GO:0035871 |
|---|---|
| GO term | protein K11-linked deubiquitination |
| Ontology | biological_process |
| Synonym | protein K11-linked deubiquitinylation; protein K11-linked deubiquitylation |
| Major function | Removal of K11-linked polyubiquitin chains from substrate proteins |
| Key enzymes | Cezanne (OTUD7B), USP38, USP32, USP19, USP52, USP7, RNF40 |
| Substrates | HIF1α, BRCA1, YAP, PKM2, KDM6A |
| Associated processes | Cell cycle regulation, hypoxia signaling, DNA repair, ferroptosis, glycolysis |
| Disease relevance | Cancer, osteoarthritis, coronavirus susceptibility, metabolic disorders |
What Is GO:0035871?
GO:0035871 is defined as a protein deubiquitination process in which a K11-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 11 of the ubiquitin monomers, is removed from a protein. In other words, it is the enzymatic reversal of K11-linked polyubiquitination, typically mediated by deubiquitinating enzymes (DUBs) that cleave the isopeptide bond between the C-terminal glycine of one ubiquitin and lysine 11 of the next ubiquitin in the chain.
Why Is protein K11-linked deubiquitination Important in Cell Biology?
Protein K11-linked deubiquitination is critical because K11-linked ubiquitin chains are a major signal for proteasomal degradation and cell cycle control, and their removal by DUBs determines the stability of key regulatory proteins. This process directly influences tumor suppression through BRCA1 stabilization, hypoxia adaptation via HIF1α, and metabolic reprogramming in osteoarthritis. Understanding GO:0035871 provides mechanistic insight into how cells counteract APC/C activity and maintain protein homeostasis, with broad implications for cancer therapy, immunotherapy, and inflammatory diseases.
• Regulates cell cycle progression by reversing APC/C-mediated K11-linked ubiquitination.
• Stabilizes BRCA1 to maintain genome integrity and tumor suppression.
• Enhances hypoxia signaling by deubiquitinating HIF1α at Lys769.
• Modulates ferroptosis and immunotherapy response in colorectal cancer via USP52.
• Promotes osteoarthritis pathogenesis through USP32-mediated PKM2 stabilization.
• Facilitates hepatocellular carcinoma progression by stabilizing YAP via USP19.
• Controls KDM6A homeostasis and coronavirus susceptibility through USP7 and RNF40.
• Provides a target for small-molecule inhibitors such as OTUD7B inhibitors.
• Links ubiquitin chain linkage specificity to disease-specific signaling pathways.
• Enables CRISPR-based functional studies of DUB-substrate relationships.
What Happens During protein K11-linked deubiquitination?
Recognition of K11-linked ubiquitin chains
In simple terms: The enzyme first finds and binds the specific K11-linked ubiquitin chain on a target protein.
Deubiquitinating enzymes (DUBs) that act on K11-linked chains must recognize the unique conformation of K11-linked polyubiquitin, which differs from other linkage types. Cezanne (OTUD7B) specifically binds K11-linked chains on BRCA1, allowing it to counteract APC/C and Ube2S-dependent ubiquitination. This recognition step is essential for linkage specificity and prevents off-target cleavage of other ubiquitin chains.
Catalytic cleavage of the isopeptide bond
In simple terms: The enzyme cuts the bond between ubiquitin molecules, removing the chain from the target protein.
Once bound, the DUB catalyzes the hydrolysis of the isopeptide bond between the C-terminal glycine of one ubiquitin and lysine 11 of the next ubiquitin, effectively disassembling the K11-linked chain. This reaction is mediated by the catalytic domain of the DUB, such as the OTU domain of Cezanne or the USP domain of USP38. The cleavage can remove the entire chain or trim it to monoubiquitin, depending on the enzyme and substrate context.
Substrate stabilization and downstream signaling
In simple terms: After the chain is removed, the target protein is stabilized and can carry out its function.
Removal of K11-linked chains prevents proteasomal degradation of the substrate, leading to increased protein stability and enhanced signaling. For example, USP38-mediated deubiquitination of HIF1α at Lys769 increases HIF1α levels and enhances hypoxia signaling. Similarly, Cezanne stabilizes BRCA1, promoting DNA repair and genome stability. In osteoarthritis, USP32 stabilizes PKM2 to modulate glycolytic metabolism in chondrocytes.
Regulation by opposing E3 ligases
In simple terms: The process is balanced by enzymes that add K11-linked chains, creating a dynamic cycle.
K11-linked deubiquitination is counteracted by E3 ligases such as APC/C, which together with Ube2S assembles K11-linked chains on substrates. This dynamic interplay determines the net ubiquitination state of a protein. For instance, the balance between APC/C-mediated ubiquitination and Cezanne-mediated deubiquitination controls BRCA1 levels during the cell cycle. Similarly, USP7 and RNF40 antagonistically regulate KDM6A homeostasis through ubiquitin switching.
Linkage-specific DUBs and their targets
In simple terms: Different enzymes remove K11-linked chains from different target proteins.
Several DUBs have been implicated in K11-linked deubiquitination, including Cezanne (OTUD7B), USP38, USP32, USP19, USP52, and USP7. Each DUB exhibits substrate specificity: USP38 targets HIF1α, Cezanne targets BRCA1, USP32 targets PKM2, USP19 targets YAP, USP52 regulates ferroptosis via the Hippo-YAP pathway, and USP7 regulates KDM6A. This diversity allows precise control of distinct signaling pathways.
Key Genes Involved in GO:0035871 protein K11-linked deubiquitination
The following genes encode enzymes and substrates directly implicated in protein K11-linked deubiquitination (GO:0035871) based on published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| OTUD7B (Cezanne) | K11-linked DUB that stabilizes BRCA1 | Counteracts APC/C and Ube2S; tumor suppression |
| USP38 | Deubiquitinates HIF1α at Lys769 | Enhances hypoxia signaling |
| USP32 | Stabilizes PKM2 | Promotes osteoarthritis via glycolytic metabolism |
| USP19 | Stabilizes YAP | Facilitates hepatocellular carcinoma progression |
| USP52 | Inhibits ferroptosis via Hippo-YAP | Blocks immunotherapy in colorectal cancer |
| USP7 | Regulates KDM6A homeostasis | Antagonizes RNF40; coronavirus susceptibility |
| RNF40 | E3 ligase opposing USP7 | Ubiquitin switching on KDM6A |
| BRCA1 | Substrate of Cezanne | DNA repair and genome stability |
| HIF1α | Substrate of USP38 | Hypoxia adaptation |
| PKM2 | Substrate of USP32 | Glycolytic metabolism in chondrocytes |
| YAP | Substrate of USP19 | Hippo signaling and cancer |
| KDM6A | Substrate of USP7/RNF40 | Epigenetic regulation and coronavirus entry |
| APC/C | E3 ligase assembling K11-linked chains | Cell cycle control |
| Ube2S | E2 enzyme for K11-linked chain elongation | APC/C-dependent ubiquitination |
| OTUD7B inhibitor | Small-molecule inhibitor | Targeting K11-linked deubiquitination |
How Is protein K11-linked deubiquitination Regulated?
Protein K11-linked deubiquitination is regulated at multiple levels. The opposing activities of E3 ligases such as APC/C and DUBs like Cezanne create a dynamic equilibrium that controls substrate stability. Cell cycle-dependent activation of APC/C determines when K11-linked chains are assembled, while DUB expression and localization dictate their removal. In hypoxia, USP38 expression and activity are modulated to stabilize HIF1α. In osteoarthritis, inflammatory cues may influence USP32-mediated PKM2 stabilization. Additionally, small-molecule inhibitors of OTUD7B can modulate K11-linked deubiquitination, offering a pharmacological handle. The interplay between USP7 and RNF40 on KDM6A illustrates how ubiquitin switching regulates substrate fate.
protein K11-linked deubiquitination and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| OTUD7B (Cezanne) | Breast and ovarian cancer (BRCA1 stability) | BRCA1-mutant cancer cell lines with OTUD7B knockout |
| USP38 | Hypoxia-related diseases (HIF1α signaling) | HIF1α reporter cells under hypoxia with USP38 KO |
| USP32 | Osteoarthritis (PKM2/glycolysis) | Chondrocyte cell lines with USP32 overexpression |
| USP19 | Hepatocellular carcinoma (YAP stability) | Liver cancer cell lines with USP19 knockout |
| USP52 | Colorectal cancer (ferroptosis/immunotherapy) | Colorectal cancer cells with USP52 KO and ferroptosis inducers |
| USP7/RNF40 | Coronavirus susceptibility (KDM6A) | Airway epithelial cells with USP7 or RNF40 KO |
Cancer
Dysregulation of K11-linked deubiquitination contributes to cancer through altered stability of oncoproteins and tumor suppressors. Cezanne stabilizes BRCA1 by counteracting APC/C and Ube2S-dependent K11-linked ubiquitination, and loss of this regulation may impair DNA repair and promote tumorigenesis. USP19 stabilizes YAP to facilitate hepatocellular carcinoma progression, while USP52 inhibits ferroptosis via the Hippo-YAP pathway and blocks immunotherapy in colorectal cancer. These findings highlight K11-linked deubiquitination as a potential therapeutic target in multiple cancers.
Hypoxia and metabolic disorders
USP38 promotes deubiquitination of K11-linked polyubiquitination of HIF1α at Lys769 to enhance hypoxia signaling, linking GO:0035871 to oxygen sensing and metabolic adaptation. In osteoarthritis, USP32 modulates PKM2 stability and glycolytic metabolism in chondrocytes, suggesting a role for K11-linked deubiquitination in joint degeneration. These examples demonstrate the broad impact of this process on cellular metabolism and disease.
Infectious disease and epigenetics
Antagonistic ubiquitin switching by USP7 and RNF40 orchestrates KDM6A homeostasis to license coronavirus susceptibility, implicating K11-linked deubiquitination in viral entry and epigenetic regulation. This connection expands the disease relevance of GO:0035871 beyond cancer and metabolism.
From protein K11-linked deubiquitination-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does knockout of a DUB affect K11-linked chain levels on a substrate? | CRISPR knockout cell line (e.g., OTUD7B KO) |
| Does a specific lysine mutation on the substrate prevent deubiquitination? | Point-mutation knock-in (e.g., HIF1α Lys769Arg) |
| Does tagging the substrate allow tracking of K11-linked ubiquitination? | Tagged knock-in (e.g., HA-BRCA1) |
| Does overexpression of a DUB enhance substrate stability? | Overexpression cell line (e.g., USP38 overexpression) |
| Can a small-molecule inhibitor block K11-linked deubiquitination? | OTUD7B inhibitor treatment in cancer cells |
| Does K11-linked deubiquitination regulate viral entry? | USP7/RNF40 knockout in coronavirus infection models |
How to Study the protein K11-linked deubiquitination Process
| Method | What It Measures | Typical Application |
|---|---|---|
| K11-linkage-specific immunoblot | Levels of K11-linked ubiquitin chains on substrate | Monitoring DUB activity in cells |
| Mass spectrometry | Ubiquitination sites and chain linkage | Mapping K11-linked substrates |
| CRISPR knockout screen | Genes affecting substrate stability | Identifying DUBs in K11-linked deubiquitination |
| In vitro deubiquitination assay | Catalytic activity and linkage specificity | Testing DUB inhibitors |
| Co-immunoprecipitation | DUB-substrate interaction | Validating binding of Cezanne to BRCA1 |
| RNA-seq | Transcriptional changes upon DUB manipulation | Assessing downstream signaling |
| Proximity ligation assay | In situ interaction and localization | Visualizing DUB-substrate complexes |
| Small-molecule inhibitor screening | Pharmacological inhibition of DUBs | Drug discovery for OTUD7B |
Ubiquitin chain-specific antibodies and immunoblotting
K11-linked ubiquitination can be detected using linkage-specific antibodies that recognize K11-linked polyubiquitin chains. This method allows researchers to monitor changes in K11-linked chain levels on substrates after DUB knockout or overexpression. For example, USP38-mediated deubiquitination of HIF1α was demonstrated by immunoblotting with K11-linkage-specific antibodies.
Mass spectrometry-based proteomics
Mass spectrometry can identify ubiquitination sites and quantify K11-linked chain abundance on target proteins. This approach has been used to map the ubiquitination landscape and determine linkage specificity of DUBs such as Cezanne. Proteomics also enables global analysis of K11-linked deubiquitination substrates.
CRISPR-based functional screens
CRISPR knockout libraries can be used to screen for DUBs that regulate K11-linked deubiquitination of a specific substrate. This method identifies genes whose loss alters substrate stability or downstream signaling. For instance, CRISPR screens have implicated USP7 and RNF40 in KDM6A homeostasis.
In vitro deubiquitination assays
Recombinant DUBs and K11-linked ubiquitinated substrates can be used in cell-free assays to measure catalytic activity and linkage specificity. Such assays confirmed that Cezanne directly cleaves K11-linked chains from BRCA1. They also allow testing of small-molecule inhibitors like OTUD7B inhibitors.
How CRISPR Can Be Used to Study GO:0035871 protein K11-linked deubiquitination
Knockout
CRISPR knockout of DUBs such as OTUD7B, USP38, or USP32 allows researchers to assess their role in K11-linked deubiquitination. For example, OTUD7B knockout increases K11-linked ubiquitination of BRCA1 and reduces its stability. USP38 knockout decreases HIF1α stability under hypoxia. These models are essential for establishing causality.
Point Mutation
Point mutations can be introduced into the ubiquitination site of a substrate to prevent K11-linked chain attachment. For instance, mutating HIF1α Lys769 to arginine blocks USP38-mediated deubiquitination and alters hypoxia signaling. Such models help define the specific lysine residues involved in K11-linked deubiquitination.
Knock-in
Knock-in of tagged versions of substrates (e.g., HA-BRCA1) enables tracking of K11-linked ubiquitination and deubiquitination in endogenous contexts. Tagged knock-in models are valuable for studying dynamic changes in chain linkage without overexpression artifacts.
Overexpression
Overexpression of DUBs such as USP38 or USP32 can enhance substrate stability and amplify downstream signaling. Overexpression models are useful for gain-of-function studies and for testing whether a DUB is sufficient to drive a phenotype, such as osteoarthritis-related metabolic changes.
How EDITGENE Supports protein K11-linked deubiquitination Research
Researchers studying protein K11-linked deubiquitination-related genes often need to determine whether a candidate gene is causally involved in substrate stabilization, signaling, or disease progression. EDITGENE provides comprehensive CRISPR-based services to enable such functional studies with high precision and reproducibility.
Contact EDITGENE today to design your custom CRISPR model for protein K11-linked deubiquitination research.
Frequently Asked Questions About protein K11-linked deubiquitination
What is protein K11-linked deubiquitination?
It is the biological process (GO:0035871) that removes K11-linked polyubiquitin chains from target proteins, reversing a specific type of ubiquitination.
What genes are involved in protein K11-linked deubiquitination?
Key genes include OTUD7B (Cezanne), USP38, USP32, USP19, USP52, USP7, and RNF40, as well as substrates like BRCA1, HIF1α, PKM2, YAP, and KDM6A.
Which enzyme removes K11-linked ubiquitin chains?
Cezanne (OTUD7B) is a well-characterized DUB that specifically removes K11-linked chains from BRCA1.
How is K11-linked deubiquitination linked to cancer?
It stabilizes tumor suppressors like BRCA1 and oncoproteins like YAP, influencing cancer progression and therapy response.
What is the role of USP38 in K11-linked deubiquitination?
USP38 deubiquitinates HIF1α at Lys769, enhancing hypoxia signaling.
Can K11-linked deubiquitination be targeted by drugs?
Yes, small-molecule inhibitors of OTUD7B have been discovered and validated, showing potential for pharmacological modulation.
What methods are used to study K11-linked deubiquitination?
Common methods include K11-linkage-specific immunoblotting, mass spectrometry, CRISPR screens, and in vitro deubiquitination assays.
What diseases are associated with K11-linked deubiquitination?
Cancer, osteoarthritis, hypoxia-related diseases, and coronavirus susceptibility have been linked to this process.
How does USP32 contribute to osteoarthritis?
USP32 stabilizes PKM2 and modulates glycolytic metabolism in chondrocytes, promoting osteoarthritis.
What is the relationship between USP7 and KDM6A?
USP7 and RNF40 antagonistically regulate KDM6A homeostasis through ubiquitin switching, affecting coronavirus susceptibility.
Conclusion
Protein K11-linked deubiquitination (GO:0035871) is a specialized biological process that reverses K11-linked polyubiquitination, thereby controlling the stability of critical regulatory proteins such as BRCA1, HIF1α, and YAP. Its dysregulation is implicated in cancer, osteoarthritis, and infectious disease, making it an attractive target for therapeutic intervention. Advances in CRISPR-based models and linkage-specific assays continue to unravel the complex interplay between DUBs and E3 ligases in this pathway.
References
- 1. Wang R et al.. 2024. USP38 promotes deubiquitination of K11-linked polyubiquitination of HIF1α at Lys769 to enhance hypoxia signaling.. J Biol Chem 300(1):105532 PMID: 38072059
- 2. Zhou J et al.. 2025. USP52 inhibits cell ferroptosis via Hippo-YAP pathway and blocks immunotherapy in colorectal cancer.. J Biol Chem 301(11):110725 PMID: 40962058
- 3. Zhao J et al.. 2025. USP32 promotes temporomandibular joint osteoarthritis by modulating PKM2 stability and glycolytic metabolism in chondrocytes.. Cell Death Dis 16(1):781 PMID: 41184228
- 4. Tian Z et al.. 2023. The deubiquitinating enzyme USP19 facilitates hepatocellular carcinoma progression through stabilizing YAP.. Cancer Lett 577:216439 PMID: 37832781
- 5. Wang L et al.. 2025. The deubiquitinating enzyme Cezanne stabilizes BRCA1 by counteracting APC/C and Ube2S-dependent Lys11-linked ubiquitination.. PLoS Biol 23(12):e3003545 PMID: 41359628
- 6. Bonacci T et al.. 2019. Impressionist portraits of mitotic exit: APC/C, K11-linked ubiquitin chains and Cezanne.. Cell Cycle 18(6-7):652-660 PMID: 30874463
- 7. Chen J et al.. 2023. AtomNet-Aided OTUD7B Inhibitor Discovery and Validation.. Cancers (Basel) 15(2) PMID: 36672466
- 8. Huang MZ et al.. 2026. Antagonistic Ubiquitin Switching by USP7 and RNF40 Orchestrates KDM6A Homeostasis to License Coronavirus Susceptibility.. Adv Sci (Weinh) 13(23):e18058 PMID: 41691482
