How p97-Associated Deubiquitinases Protect Our Cells
Exploring the delicate balance between protein destruction and rescue in cellular quality control
Imagine a bustling factory operating within every cell of your body—this is the endoplasmic reticulum (ER), where thousands of proteins are synthesized, folded, and prepared for their specific functions. Like any quality-driven production line, this cellular factory has a crucial quality control system that identifies and removes defective products. When this system fails, misfolded proteins accumulate, leading to serious diseases ranging from cancer to neurodegenerative disorders.
The ER functions as a protein factory, synthesizing and folding thousands of proteins essential for cellular function.
Specialized systems identify and remove misfolded proteins to prevent cellular damage and disease.
At the heart of this quality control process lies a fascinating molecular machine called p97 (also known as VCP or Cdc48) and its unexpected partners—deubiquitinases (DUBs). These enzymes possess the seemingly contradictory ability to remove the very "destroy me" tags that mark defective proteins for elimination. This article explores how this cellular contradiction is resolved and reveals the delicate balance these enzymes maintain to keep our cells healthy 1 4 .
Cells employ a sophisticated process called ER-associated degradation (ERAD) to handle misfolded proteins in the endoplasmic reticulum. This system identifies defective proteins, marks them for destruction, and transports them to the cellular recycling center—the proteasome 1 .
Chaperone proteins identify misfolded proteins in the ER 1 .
p97 is a hexameric AAA+ ATPase—a molecular machine that converts chemical energy from ATP into mechanical force. It functions as a "segregase" that can physically extract proteins from cellular structures like membranes, protein complexes, or chromatin 1 2 .
A complex molecular machine with multiple functional domains working in coordination.
In ERAD, p97 collaborates with a dimeric cofactor complex called Ufd1-Npl4 that helps recognize ubiquitinated substrates. Using energy from ATP hydrolysis, p97 extracts these marked proteins from the ER membrane, making them accessible to the proteasome 1 7 .
For years, scientists were puzzled by a seeming contradiction: why would p97 associate with deubiquitinases—enzymes that remove ubiquitin chains—when ubiquitination is essential for targeting proteins to the proteasome? This would be like a recycling plant hiring workers to remove the "recycle me" labels from materials destined for processing 1 4 .
Deubiquitinases remove the very tags that mark proteins for destruction.
They fine-tune the degradation process rather than simply opposing it.
Research has revealed that these p97-associated deubiquitinases (PADs) don't simply oppose degradation but instead fine-tune the process. They play regulatory roles that actually enhance the efficiency of protein quality control through several potential mechanisms:
Notable p97-associated deubiquitinases include ataxin-3 and YOD1, which have been shown to positively regulate ERAD despite their ubiquitin-removing capabilities 1 4 .
While many p97-associated deubiquitinases function in ERAD, recent research has revealed their importance in other cellular processes. A landmark 2025 study published in Nature Communications examined how USP37 prevents premature disassembly of replication machinery during DNA synthesis—a process with parallels to ERAD in its use of p97 and ubiquitination 5 .
The research team employed sophisticated techniques to understand how USP37 regulates the replication process:
Systematic knockdown of various deubiquitinases in human cells to assess function 5 .
Precise measurement of chromatin-bound MCM complexes during cell cycle stages 5 .
Interaction studies and deubiquitination assays to demonstrate direct mechanisms 5 .
The study yielded several crucial insights that advanced our understanding of deubiquitinase function:
| Parameter Measured | Control Cells | USP37-Depleted Cells | Significance |
|---|---|---|---|
| Chromatin-bound MCM | Bimodal distribution | Nearly unimodal distribution | Complete replisome disassembly |
| EdU incorporation | Normal levels | Substantially reduced | Impaired S phase progression |
| MCM7 ubiquitination | Baseline levels | Significantly increased | Failure to antagonize CRL2LRR1 |
Depleting USP37 resulted in the lowest levels of chromatin-bound MCM complexes among all DUBs tested, indicating premature replisome disassembly 5 .
USP37 interacts with the CMG helicase complex and deubiquitinates MCM7, directly counteracting the ubiquitination that triggers replisome disassembly 5 .
This research demonstrates how deubiquitinases can precisely regulate fundamental cellular processes by counterbalancing ubiquitin signals. The parallels between replisome disassembly and ERAD—both employing p97 to process ubiquitinated substrates—suggest similar regulatory mechanisms may operate in protein quality control at the ER.
Studying complex cellular processes like p97-mediated protein quality control requires specialized research tools. The table below highlights key reagents that scientists use to unravel these mechanisms:
| Research Tool | Function/Description | Key Applications |
|---|---|---|
| CB-5083 | Potent, selective p97 ATPase inhibitor (IC₅₀ = 11 nM) 3 | Studying p97 inhibition in cancer cells; induces ER stress 2 |
| NMS-873 | Allosteric p97 inhibitor (IC₅₀ = 30 nM) 3 | Non-ATP competitive inhibition; useful for mechanistic studies |
| Eeyarestatin I | ERAD and p97-associated deubiquitination inhibitor 3 | Blocks ataxin-3-dependent deubiquitination; protein translocation studies |
| DBeQ | Selective, reversible p97 inhibitor (IC₅₀ = 1.5-1.6 μM) 3 | Early-stage p97 research; moderate potency for preliminary studies |
| siRNA Libraries | Targeted gene knockdown tools | Functional screens for DUB involvement in cellular processes 5 |
| Ubiquitin Probes | Activity-based probes for DUB profiling | Identifying active deubiquitinases and their specificity 6 |
The ongoing development of more specific research tools continues to drive our understanding of p97 and its associated deubiquitinases, with implications for treating cancer, neurodegenerative diseases, and other conditions linked to protein quality control failures.
The fundamental research on p97-associated deubiquitinases has significant translational potential, particularly in cancer therapeutics. Cancer cells typically exhibit high rates of protein synthesis, making them particularly dependent on protein quality control systems like ERAD. This dependency creates a therapeutic vulnerability that can be exploited 2 .
This first-in-class p97 inhibitor advanced to Phase I clinical trials, establishing proof-of-concept that targeting p97 has clinical potential 2 .
Phase I Clinical Trials| Inhibitor Name | Mechanism of Action | Development Stage | Potential Applications |
|---|---|---|---|
| CB-5083 | ATP-competitive, inhibits D2 domain | Phase I clinical trials | Solid tumors, hematological malignancies |
| CB-5339 | ATP-competitive, improved properties | Clinical trials | Acute myeloid leukemia |
| NMS-873 | Allosteric inhibitor | Preclinical research | Mechanism studies, combination therapies |
| ML240 | ATP-competitive inhibitor | Preclinical research | Tool compound for target validation |
Beyond cancer, understanding p97-associated deubiquitinases has implications for neurodegenerative diseases. Mutations in p97 have been linked to several neurodegenerative conditions, and proper regulation of protein quality control is essential for preventing toxic protein aggregation that characterizes diseases like Alzheimer's and Parkinson's 2 .
The study of p97-associated deubiquitinases reveals a fascinating principle in cell biology: cellular processes often depend on carefully balanced opposing forces. Rather than simply promoting or preventing degradation, these enzymes fine-tune the process, ensuring that protein quality control is both efficient and accurate.
Opposing forces work in harmony to maintain cellular health.
Fine-tuning ensures accurate protein quality control.
Targeting these processes offers new treatment avenues.
As research continues to unravel the complexities of these molecular guardians, we gain not only fundamental insights into cellular function but also new opportunities for therapeutic intervention in diseases ranging from cancer to neurodegenerative disorders. The precise regulation of protein quality control—with deubiquitinases serving as crucial moderators—represents an elegant solution to the cellular challenge of maintaining integrity in the face of constant protein production and inevitable folding errors.