GO:0032780 negative regulation of ATP-dependent activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0032780 describes any process that stops or reduces the rate of an ATP-dependent activity, including inhibition of ATPase and adenosinetriphosphatase reactions.
• ATP-dependent activities include chromatin remodeling motors, AAA+ proteases such as LONP1 and PSMD14, and ion channels such as TRPV1.
• Negative regulation can be direct (ATP binding, inhibitory proteins, feedback loops) or indirect (limiting substrate, cofactor availability, or enzyme abundance).
• The NRF2-p97-NRF2 negative feedback loop illustrates how ATP-dependent protein handling is restrained to prevent oxidative stress.
• Dysregulated negative regulation of ATP-dependent activity contributes to metabolic dysfunction-associated steatohepatitis, pulmonary hypertension, and triple-negative breast cancer.
• CRISPR knockout, point-mutation, knock-in, and overexpression models allow causal testing of ATPase regulators in disease and cell biology.
Description
GO:0032780, negative regulation of ATP-dependent activity, is a biological process ontology term defined as any process that stops or reduces the rate of an ATP-dependent activity. ATP-dependent activities are reactions that require the free energy of ATP hydrolysis to perform mechanical, chemical, or transport work, and they include ATPase motors, chaperones, proteases, kinases, and ion pumps. Because these activities consume cellular energy and drive essential processes, their negative regulation is critical for metabolic balance, stress responses, and tissue homeostasis. Researchers study GO:0032780 to understand how cells switch off ATP-consuming machines, how this control fails in disease, and how it can be targeted therapeutically. The term is distinct from general ATPase inhibition because it encompasses any upstream process that reduces the rate of an ATP-dependent activity, including transcriptional, post-translational, and feedback mechanisms.
negative regulation of ATP-dependent activity At A Glance
| GO ID | GO:0032780 |
|---|---|
| GO term | negative regulation of ATP-dependent activity |
| Ontology | biological_process |
| Definition | Any process that stops or reduces the rate of an ATP-dependent activity. |
| Synonym | down regulation of ATPase activity; down-regulation of ATPase activity; downregulation of ATPase activity; inhibition of ATPase activity; negative regulation of adenosinetriphosphatase activity; negative regulation of ATPase activity |
| Major function | Restrains ATP-consuming enzymes and machines to balance energy use and prevent excessive or inappropriate activity |
| Example ATP-dependent activities | Chromatin remodeling, AAA+ proteolysis, ion channel gating, protein degradation |
| Disease relevance | Metabolic liver disease, pulmonary hypertension, and cancer |
| Research methods | CRISPR KO, point mutation, knock-in, overexpression, ATPase assays, proteomics |
What Is GO:0032780?
In practical terms, GO:0032780 covers any cellular process that decreases the rate of an activity that depends on ATP. This includes direct inhibition of ATPase enzymes, downregulation of their expression, sequestration of their substrates or cofactors, and negative feedback loops that limit ATP-dependent protein handling. The QuickGO synonyms include down regulation of ATPase activity, inhibition of ATPase activity, and negative regulation of adenosinetriphosphatase activity, reflecting the broad enzymatic scope of the term.
Why Is negative regulation of ATP-dependent activity Important in Cell Biology?
Negative regulation of ATP-dependent activity is important because ATP-dependent machines consume a large fraction of cellular energy and can cause damage if left unchecked. For example, the ATP-dependent Lon protease LONP1 is negatively regulated in metabolic dysfunction-associated steatohepatitis, and decreased LONP1 expression exacerbates liver fibrosis via elevated orotic acid levels. In endothelial cells, inactivation of the ATP-dependent malic enzyme 1 alleviates pulmonary hypertension, showing that reducing an ATP-dependent activity can be protective. In triple-negative breast cancer, targeting the ATP-dependent PSMD14 combined with arachidonic acid induces synthetic lethality through FADS1 m6A modification. These examples demonstrate that GO:0032780 is not a passive brake but an active, disease-relevant control layer.
• Controls energy homeostasis by limiting ATP-consuming enzymes and motors.
• Prevents oxidative stress through feedback loops such as NRF2-p97-NRF2.
• Regulates chromatin remodeling and gene expression programs.
• Modulates ion channel activity, including TRPV1 regulation by intracellular ATP.
• Influences proteostasis through AAA+ proteases such as LONP1 and PSMD14.
• Contributes to metabolic liver disease, pulmonary hypertension, and cancer.
• Provides therapeutic targets for synthetic lethality strategies.
• Can be studied with CRISPR KO, point mutation, knock-in, and overexpression models.
What Happens During negative regulation of ATP-dependent activity?
Recognition of the ATP-dependent target
In simple terms: First, the cell must identify which ATP-consuming machine to restrain.
Negative regulation begins with recognition of the ATP-dependent enzyme or complex. This can occur through direct protein-protein interaction, post-translational modification, or changes in substrate availability. For example, the NRF2-p97-NRF2 negative feedback loop involves p97, an ATP-dependent segregase, in regulating NRF2 stability. In circadian chromatin regulation, ATP-dependent chromatin remodeling activities are targeted to control gene expression.
Direct inhibition of ATPase activity
In simple terms: The regulator blocks the enzyme from using ATP.
Direct inhibition reduces the rate of ATP hydrolysis or coupling to work. Intracellular ATP itself can regulate TRPV1 channel activities in the absence of capsaicin, showing that ATP levels can act as a negative regulator of an ATP-dependent process. ATP-dependent chromatin remodeling activities are also subject to negative regulation that affects nucleosome positioning and transcription.
Downregulation of enzyme abundance
In simple terms: The cell makes less of the ATP-dependent enzyme.
Reduced expression of an ATP-dependent enzyme is a common mechanism of negative regulation. Decreased LONP1 expression exacerbates MASH-induced liver fibrosis via elevated orotic acid levels, demonstrating that lower LONP1 abundance reduces ATP-dependent proteolysis and worsens disease. In endothelial cells, inactivation of malic enzyme 1 alleviates pulmonary hypertension, indicating that reducing an ATP-dependent metabolic enzyme can be beneficial.
Feedback loops and pathway crosstalk
In simple terms: The product of a pathway turns the pathway down.
Negative feedback loops are central to GO:0032780. The NRF2-p97-NRF2 negative feedback loop restrains ATP-dependent protein handling to prevent oxidative stress. Circadian chromatin regulation integrates ATP-dependent remodeling with daily rhythms, providing temporal control of ATP-dependent activities. Targeting PSMD14 combined with arachidonic acid induces synthetic lethality via FADS1 m6A modification in triple-negative breast cancer, illustrating how disrupting an ATP-dependent activity can be exploited therapeutically.
Physiological consequences
In simple terms: The result is a change in cell behavior.
The downstream effects of negative regulation include altered energy balance, changed gene expression, and modified stress responses. In Pseudomonas syringae pv. tabaci 11528, the ATP-dependent Lon protease negatively regulates pathogenesis, showing that ATP-dependent activities can control virulence. In human cells, negative regulation of ATP-dependent activities affects fibrosis, vascular remodeling, and tumor survival.
Key Genes Involved in GO:0032780 negative regulation of ATP-dependent activity
The following genes and proteins are experimentally linked to negative regulation of ATP-dependent activity or to ATP-dependent activities that are subject to negative regulation.
| Gene | Major Role | Research Relevance |
|---|---|---|
| LONP1 | ATP-dependent Lon protease in mitochondria | Decreased expression exacerbates MASH-induced liver fibrosis via orotic acid |
| ME1 | ATP-dependent malic enzyme 1 | Inactivation in endothelial cells alleviates pulmonary hypertension |
| PSMD14 | ATP-dependent deubiquitinase in the 26S proteasome | Targeting with arachidonic acid induces synthetic lethality in TNBC |
| TRPV1 | ATP-regulated ion channel | Intracellular ATP regulates channel activities without capsaicin |
| NRF2 | Transcription factor in oxidative stress response | Part of the NRF2-p97-NRF2 negative feedback loop |
| p97/VCP | ATP-dependent segregase | Regulates NRF2 stability in a negative feedback loop |
| FADS1 | Fatty acid desaturase | m6A modification linked to PSMD14 targeting in TNBC |
| Chromatin remodeling ATPases | ATP-dependent nucleosome remodeling | Subject to negative regulation in circadian chromatin |
| Lon protease (bacterial) | ATP-dependent protease | Negatively regulates pathogenesis in Pseudomonas syringae |
| ATPase motors | General ATP-hydrolyzing enzymes | Targets of negative regulation in multiple pathways |
| Proteasome subunits | ATP-dependent protein degradation | PSMD14 is a therapeutic target in cancer |
| Mitochondrial proteases | ATP-dependent mitochondrial quality control | LONP1 links to liver fibrosis |
| Metabolic enzymes | ATP-dependent metabolic reactions | ME1 links to pulmonary hypertension |
| Ion channels | ATP-sensitive transport | TRPV1 is regulated by intracellular ATP |
| Transcription factors | Regulate gene expression | NRF2 is controlled by ATP-dependent p97 |
| Circadian regulators | Control daily chromatin states | ATP-dependent remodeling is negatively regulated |
How Is negative regulation of ATP-dependent activity Regulated?
Negative regulation of ATP-dependent activity is itself regulated at multiple levels. The NRF2-p97-NRF2 negative feedback loop shows that ATP-dependent protein handling can be restrained by its own substrates to prevent oxidative stress. Circadian chromatin regulation provides temporal control, linking ATP-dependent remodeling to daily rhythms. In disease, reduced LONP1 expression lowers ATP-dependent proteolysis and elevates orotic acid, indicating that enzyme abundance is a key regulatory node. Inactivation of ME1 in endothelial cells alleviates pulmonary hypertension, showing that metabolic context can determine whether negative regulation is protective or harmful. Targeting PSMD14 combined with arachidonic acid induces synthetic lethality, demonstrating that pharmacological interruption of an ATP-dependent activity can be a therapeutic strategy.
negative regulation of ATP-dependent activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| LONP1 | MASH-induced liver fibrosis | LONP1 knockout or knockdown hepatocytes; overexpression rescue |
| ME1 | Pulmonary hypertension | Endothelial cell-specific ME1 knockout; overexpression |
| PSMD14 | Triple-negative breast cancer | PSMD14 knockout or point-mutation TNBC cells; drug combination |
| NRF2/p97 | Oxidative stress | NRF2 or p97 knockout; feedback loop reporters |
| TRPV1 | Pain and sensory signaling | TRPV1 point-mutation or knockout; ATP sensitivity assays |
Metabolic dysfunction-associated steatohepatitis and liver fibrosis
Decreased LONP1 expression exacerbates MASH-induced liver fibrosis via elevated orotic acid levels, linking negative regulation of an ATP-dependent protease to liver disease progression. This suggests that restoring or mimicking LONP1 negative regulation could be protective, while loss of LONP1 activity worsens fibrosis.
Pulmonary hypertension
Inactivation of malic enzyme 1 in endothelial cells alleviates pulmonary hypertension, indicating that reducing an ATP-dependent metabolic activity can reverse vascular remodeling. This positions ME1 and related ATP-dependent activities as potential targets in pulmonary vascular disease.
Triple-negative breast cancer
Targeting PSMD14 combined with arachidonic acid induces synthetic lethality via FADS1 m6A modification in triple-negative breast cancer. This demonstrates that negative regulation or pharmacological inhibition of an ATP-dependent proteasome subunit can selectively kill cancer cells.
Oxidative stress and inflammation
The NRF2-p97-NRF2 negative feedback loop restrains ATP-dependent protein handling to prevent oxidative stress, linking GO:0032780 to redox homeostasis and inflammation. Dysregulation of this loop may contribute to chronic inflammatory diseases.
From negative regulation of ATP-dependent activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of an ATP-dependent enzyme worsen liver fibrosis? | LONP1 knockout or knockdown in hepatocytes |
| Does reducing an ATP-dependent metabolic enzyme alleviate pulmonary hypertension? | Endothelial ME1 knockout or overexpression |
| Can inhibition of an ATP-dependent proteasome subunit induce synthetic lethality? | PSMD14 knockout or point-mutation in TNBC cells |
| How does ATP regulate ion channel activity? | TRPV1 point-mutation or knockout with ATP sensitivity assays |
| How is ATP-dependent chromatin remodeling negatively regulated? | Knock-in of tagged remodeling ATPases; circadian time-course |
| What is the role of ATP-dependent proteases in pathogenesis? | Bacterial Lon protease knockout in Pseudomonas syringae |
How to Study the negative regulation of ATP-dependent activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| ATPase assay | Rate of ATP hydrolysis | Testing negative regulators of LONP1, PSMD14, TRPV1 |
| CRISPR knockout | Loss-of-function phenotype | Validating causal roles of ATP-dependent enzymes |
| Point mutation | Specific residue function | Dissecting catalytic or regulatory sites |
| Knock-in tagging | Protein localization and interactions | Tracking ATP-dependent enzymes in cells |
| Overexpression | Gain-of-function effects | Testing whether increased activity worsens disease |
| RNA-seq | Transcriptome changes | Downstream effects of negative regulation |
| Proteomics | Protein interactions and abundance | Identifying feedback loop components |
| Metabolomics | Metabolite levels such as orotic acid | Linking ATP-dependent activity to metabolism |
ATPase activity assays
Direct measurement of ATP hydrolysis rates is the primary way to detect negative regulation of ATP-dependent activity. These assays can be coupled to specific enzymes such as LONP1, PSMD14, or TRPV1 to test whether a candidate regulator reduces activity.
CRISPR-based genetic perturbation
Knockout, point-mutation, knock-in, and overexpression models allow causal testing of genes involved in GO:0032780. For example, LONP1 knockout exacerbates fibrosis, ME1 knockout alleviates pulmonary hypertension, and PSMD14 targeting induces synthetic lethality.
Proteomics and interactomics
Affinity purification and mass spectrometry can identify proteins that associate with ATP-dependent enzymes and mediate their negative regulation. The NRF2-p97 interaction is a paradigm for such feedback loops.
Transcriptomics and epigenomics
RNA-seq and chromatin accessibility assays reveal how negative regulation of ATP-dependent chromatin remodeling affects gene expression programs, including circadian chromatin states.
How CRISPR Can Be Used to Study GO:0032780 negative regulation of ATP-dependent activity
Knockout
CRISPR knockout of genes encoding ATP-dependent enzymes or their regulators is used to test loss-of-function phenotypes. LONP1 knockout exacerbates MASH-induced liver fibrosis, ME1 knockout alleviates pulmonary hypertension, and PSMD14 knockout induces synthetic lethality in triple-negative breast cancer.
Point Mutation
Point mutations can dissect catalytic residues, ATP-binding sites, or regulatory phosphorylation sites in ATP-dependent enzymes. For example, mutating the ATP-binding pocket of TRPV1 or PSMD14 can reveal how ATP dependence is coupled to channel gating or proteolysis.
Knock-in
Knock-in of tags or reporters allows real-time tracking of ATP-dependent enzymes and their negative regulators. Tagged chromatin remodeling ATPases have been used to study circadian chromatin regulation.
Overexpression
Overexpression of an ATP-dependent enzyme or its negative regulator can test gain-of-function effects. Overexpressing LONP1 or ME1 can rescue or worsen disease phenotypes depending on context.
How EDITGENE Supports negative regulation of ATP-dependent activity Research
Researchers studying negative regulation of ATP-dependent activity-related genes often need to determine whether a candidate gene is causally involved in a disease or pathway. EDITGENE provides CRISPR-based cell model services that enable precise knockout, point mutation, knock-in, and overexpression of ATP-dependent enzymes and their regulators, accelerating functional validation and therapeutic target discovery.
Contact EDITGENE today to design your custom CRISPR model for negative regulation of ATP-dependent activity research.
Frequently Asked Questions About negative regulation of ATP-dependent activity
What is GO:0032780 negative regulation of ATP-dependent activity?
GO:0032780 is a biological process term defined as any process that stops or reduces the rate of an ATP-dependent activity, including inhibition of ATPase and adenosinetriphosphatase reactions.
What genes are involved in negative regulation of ATP-dependent activity?
Genes include LONP1, ME1, PSMD14, TRPV1, NRF2, p97/VCP, and chromatin remodeling ATPases, all of which have been linked to ATP-dependent activities or their negative regulation.
How is ATP-dependent activity negatively regulated?
It can be negatively regulated by direct inhibition, reduced enzyme expression, substrate limitation, and feedback loops such as the NRF2-p97-NRF2 loop.
Why is negative regulation of ATP-dependent activity important in disease?
Dysregulation contributes to liver fibrosis, pulmonary hypertension, and cancer, making it a therapeutic target.
What diseases are linked to GO:0032780?
Metabolic dysfunction-associated steatohepatitis, pulmonary hypertension, triple-negative breast cancer, and oxidative stress-related conditions.
How can CRISPR be used to study negative regulation of ATP-dependent activity?
CRISPR knockout, point mutation, knock-in, and overexpression allow causal testing of ATP-dependent enzymes and their regulators.
What methods measure negative regulation of ATP-dependent activity?
ATPase assays, proteomics, RNA-seq, metabolomics, and CRISPR screens are commonly used.
What is an example of a negative feedback loop involving ATP-dependent activity?
The NRF2-p97-NRF2 negative feedback loop restrains ATP-dependent protein handling to prevent oxidative stress.
Does intracellular ATP regulate ATP-dependent ion channels?
Yes, intracellular ATP regulates TRPV1 channel activities even in the absence of capsaicin.
How does LONP1 relate to negative regulation of ATP-dependent activity?
Decreased LONP1 expression reduces ATP-dependent proteolysis and exacerbates MASH-induced liver fibrosis via elevated orotic acid.
Conclusion
GO:0032780 negative regulation of ATP-dependent activity is a central biological process that controls energy-consuming enzymes and machines. Its dysregulation is linked to liver fibrosis, pulmonary hypertension, cancer, and oxidative stress, and it can be studied with CRISPR knockout, point mutation, knock-in, and overexpression models. Understanding this process provides mechanistic insight and therapeutic opportunities across metabolic, vascular, and oncological diseases.
References
- 1. Xu D et al.. 2026. Decreased LONP1 expression exacerbates MASH-induced liver fibrosis via elevated orotic acid levels.. J Hepatol 84(1):165-180 PMID: 40784490
- 2. Luo Y et al.. 2024. Inactivation of Malic Enzyme 1 in Endothelial Cells Alleviates Pulmonary Hypertension.. Circulation 149(17):1354-1371 PMID: 38314588
- 3. Yu Y et al.. 2025. Targeting PSMD14 combined with arachidonic acid induces synthetic lethality via FADS1 m(6)A modification in triple-negative breast cancer.. Sci Adv 11(19):eadr3173 PMID: 40344056
- 4. Zhu Q et al.. 2020. Molecular Regulation of Circadian Chromatin.. J Mol Biol 432(12):3466-3482 PMID: 31954735
- 5. Shimizu T et al.. 2022. Regulation of TRPV1 channel activities by intracellular ATP in the absence of capsaicin.. Biochim Biophys Acta Biomembr 1864(1):183782 PMID: 34555418
- 6. Havas K et al.. 2001. ATP-dependent chromatin remodeling activities.. Cell Mol Life Sci 58(5-6):673-82 PMID: 11437229
- 7. Yang HJ et al.. 2011. Negative regulation of pathogenesis in Pseudomonas syringae pv. tabaci 11528 by ATP-dependent Lon protease.. Mol Cells 32(4):317-23 PMID: 21904881
- 8. Shakya A et al.. 2023. The NRF2-p97-NRF2 negative feedback loop.. Redox Biol 65:102839 PMID: 37573837
