GO:1904262 negative regulation of TORC1 signaling: Nutrient-Sensing Pathway, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:1904262 describes any process that stops, prevents, or reduces the frequency, rate, or extent of TORC1 signaling.
• The GATOR1 complex (DEPDC5, NPRL2, NPRL3) is a major negative regulator of TORC1, acting as a GTPase-activating protein for Rag GTPases.
• Loss-of-function variants in GATOR1 genes cause epilepsy and malformations of cortical development.
• Negative regulation of TORC1 signaling is critical for metabolic homeostasis, and its dysregulation contributes to cancer, liver disease, and neurodegeneration.
• TRPML1, MAPK-regulated 4F2hc/Girdin, and protein phosphatase 6 are examples of diverse negative regulators of TORC1 signaling.
• CRISPR knockout, point mutation, and knock-in models are essential for dissecting the causal roles of negative regulators in disease.
Description
The mechanistic target of rapamycin complex 1 (TORC1) is a central regulator of cell growth and metabolism that integrates nutrient, energy, and growth factor signals. To prevent uncontrolled growth and maintain homeostasis, cells employ multiple negative regulatory mechanisms that stop, prevent, or reduce TORC1 signaling. The Gene Ontology term GO:1904262, negative regulation of TORC1 signaling, captures these processes. Understanding this term is essential for researchers studying nutrient sensing, autophagy, cancer metabolism, and neurological disorders, as its dysregulation is linked to a wide range of pathologies. This article provides a comprehensive overview of the definition, mechanisms, key genes, and research methods associated with GO:1904262, based on authoritative QuickGO data and verified PubMed literature.
negative regulation of TORC1 signaling At A Glance
| GO ID | GO:1904262 |
|---|---|
| GO term | negative regulation of TORC1 signaling |
| Ontology | biological_process |
| Synonym | inhibition of TORC1 signaling; downregulation of TORC1 signaling; negative regulation of TORC1 signal transduction |
| Major function | Stops, prevents, or reduces TORC1 signaling to maintain cellular homeostasis |
| Key regulators | GATOR1 complex (DEPDC5, NPRL2, NPRL3), TRPML1, PP6, MAPK-regulated 4F2hc/Girdin |
| Associated diseases | Epilepsy, cortical malformations, cancer, metabolic dysfunction-associated steatohepatitis |
| Research methods | CRISPR knockout/knock-in, Ribo-seq, phosphoproteomics, live-cell imaging |
What Is GO:1904262?
GO:1904262 (negative regulation of TORC1 signaling) is a biological process defined as any process that stops, prevents, or reduces the frequency, rate, or extent of TORC1 signaling. It encompasses molecular events that inhibit the activity of TORC1, a protein kinase complex that promotes anabolic processes such as protein synthesis and inhibits catabolic processes like autophagy. This negative regulation ensures that cell growth is tightly coupled to nutrient availability and environmental conditions.
Why Is negative regulation of TORC1 signaling Important in Cell Biology?
Negative regulation of TORC1 signaling is fundamental for cellular homeostasis, preventing excessive growth and promoting catabolic processes when nutrients are scarce. Its dysregulation is implicated in numerous human diseases, including epilepsy, cancer, and metabolic disorders. Studying this process provides insights into fundamental cell biology and offers potential therapeutic targets for a range of conditions.
• Prevents uncontrolled cell growth and proliferation by inhibiting TORC1 when nutrients are limited.
• Coordinates autophagy and lysosomal biogenesis with nutrient availability.
• Mutations in negative regulators like GATOR1 cause epilepsy and cortical malformations.
• Loss of negative regulation contributes to cancer progression, including liver metastasis and docetaxel resistance.
• Dysregulation is linked to metabolic dysfunction-associated steatohepatitis (MASH).
• Plays a role in healthspan and lifespan regulation, as inhibition of IL-11 signaling extends murine healthspan.
• TRPML1-mediated negative regulation supports protein homeostasis in melanoma cells.
• MAPK-regulated 4F2hc/Girdin complex provides crosstalk between amino acid signaling and TORC1.
• Protein phosphatase 6 (PP6) is a key negative regulator of TORC1 in the liver.
• Understanding these mechanisms can guide development of targeted therapies for mTOR-driven diseases.
What Happens During negative regulation of TORC1 signaling?
Sensing of Nutrient and Energy Status
In simple terms: The cell checks if it has enough nutrients and energy before deciding to grow.
Negative regulation of TORC1 signaling begins with the sensing of intracellular and extracellular cues, such as amino acid levels, glucose, and energy status. When nutrients are scarce, signaling pathways are activated that ultimately inhibit TORC1. For example, the GATOR1 complex senses amino acid sufficiency and acts on Rag GTPases to reduce TORC1 activity. Similarly, MAPK-regulated 4F2hc/Girdin complex negatively regulates amino acid signaling to TORC1.
Inhibition of Rag GTPases by GATOR1
In simple terms: A protein complex called GATOR1 acts like a brake on the Rag proteins that normally turn on TORC1.
The GATOR1 complex, composed of DEPDC5, NPRL2, and NPRL3, functions as a GTPase-activating protein (GAP) for Rag GTPases. By promoting the inactive GDP-bound state of RagA/B, GATOR1 prevents the recruitment of TORC1 to the lysosomal surface, thereby inhibiting its activation. This mechanism is a primary node for negative regulation of TORC1 signaling in response to amino acid availability.
Dephosphorylation of TORC1 Substrates by Phosphatases
In simple terms: Enzymes called phosphatases remove phosphate groups from TORC1 targets, reversing its growth-promoting signals.
Protein phosphatase 6 (PP6) directly dephosphorylates TORC1 substrates, such as S6K1 and 4E-BP1, thereby counteracting TORC1 signaling. In the liver, PP6 regulates metabolic dysfunction-associated steatohepatitis via the mTORC1 pathway. This phosphatase-mediated negative regulation ensures that TORC1 outputs are transient and reversible.
Lysosomal Calcium Signaling and TRPML1
In simple terms: Calcium released from lysosomes can put the brakes on TORC1.
TRPML1, a lysosomal calcium channel, promotes protein homeostasis in melanoma cells by negatively regulating MAPK and mTORC1 signaling. Activation of TRPML1 leads to local calcium release, which can inhibit TORC1 through mechanisms involving calcium-dependent kinases or phosphatases. This highlights the role of lysosomal signaling in negative regulation of TORC1.
Crosstalk with Other Signaling Pathways
In simple terms: Other cellular signals can also inhibit TORC1 to coordinate growth with stress responses.
Negative regulation of TORC1 signaling is integrated with other pathways, such as the MAPK pathway. The MAPK-regulated 4F2hc/Girdin complex negatively regulates amino acid signaling to TORC1. Additionally, inhibition of IL-11 signaling extends healthspan and lifespan, potentially through modulation of mTORC1 activity. These crosstalk mechanisms ensure that TORC1 activity is appropriately tuned to the overall physiological state.
Key Genes Involved in GO:1904262 negative regulation of TORC1 signaling
The following genes and proteins are key players in the negative regulation of TORC1 signaling, as supported by published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| DEPDC5 | Component of GATOR1 complex, GAP for Rag GTPases | Mutations cause epilepsy and cortical malformations |
| NPRL2 | Component of GATOR1 complex | Tumor suppressor, mutations in epilepsy |
| NPRL3 | Component of GATOR1 complex | Mutations in epilepsy |
| TRPML1 (MCOLN1) | Lysosomal calcium channel, negatively regulates mTORC1 | Melanoma protein homeostasis |
| PPP6C | Catalytic subunit of protein phosphatase 6, dephosphorylates TORC1 substrates | Metabolic dysfunction-associated steatohepatitis |
| Girdin (CCDC88A) | Scaffold protein in MAPK-regulated 4F2hc/Girdin complex | Amino acid signaling to TORC1 |
| SLC3A2 (4F2hc) | Amino acid transporter, part of 4F2hc/Girdin complex | Negative regulation of amino acid signaling |
| IL11 | Cytokine, inhibition extends healthspan and lifespan | Potential link to mTORC1 regulation |
| GPRC5A | Methylation activates mTOR signaling | Liver metastasis and docetaxel resistance in TNBC |
| RagA (RRAGA) | GTPase, target of GATOR1 | Amino acid signaling to TORC1 |
| RagB (RRAGB) | GTPase, target of GATOR1 | Amino acid signaling to TORC1 |
| RagC (RRAGC) | GTPase, partner of RagA/B | Amino acid signaling to TORC1 |
| RagD (RRAGD) | GTPase, partner of RagA/B | Amino acid signaling to TORC1 |
| mTOR | Kinase subunit of TORC1 | Central regulator of growth |
| Raptor | Scaffold protein of TORC1 | Substrate recruitment |
| S6K1 (RPS6KB1) | TORC1 substrate, promotes translation | Readout of TORC1 activity |
| 4E-BP1 (EIF4EBP1) | TORC1 substrate, inhibits translation when dephosphorylated | Readout of TORC1 activity |
How Is negative regulation of TORC1 signaling Regulated?
Negative regulation of TORC1 signaling is itself tightly regulated. The GATOR1 complex is controlled by upstream factors such as GATOR2, which inhibits GATOR1 in the presence of amino acids. Protein phosphatase 6 activity can be modulated by regulatory subunits. TRPML1 is regulated by lysosomal calcium and pH. Additionally, crosstalk with MAPK signaling via the 4F2hc/Girdin complex provides another layer of control. These regulatory mechanisms ensure that TORC1 inhibition is dynamic and responsive to cellular needs.
negative regulation of TORC1 signaling and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| DEPDC5 | Epilepsy, cortical malformations | Knockout mouse, patient-derived iPSCs |
| NPRL2 | Epilepsy, cancer | Knockout cell lines, xenograft models |
| NPRL3 | Epilepsy | Knockout zebrafish, mouse models |
| PPP6C | Metabolic dysfunction-associated steatohepatitis | Liver-specific knockout mouse |
| TRPML1 | Melanoma protein homeostasis | Knockout melanoma cell lines |
| GPRC5A | Triple-negative breast cancer metastasis | Methylation-specific knockout, overexpression |
Epilepsy and Cortical Malformations
Loss-of-function variants in GATOR1 complex genes (DEPDC5, NPRL2, NPRL3) are associated with a spectrum of epilepsy-related phenotypes, including focal epilepsy and malformations of cortical development. These mutations impair the negative regulation of TORC1 signaling, leading to hyperactive mTORC1 and neuronal hyperexcitability.
Cancer
Dysregulation of negative regulation of TORC1 signaling contributes to cancer. For example, methylation of GPRC5A promotes liver metastasis and docetaxel resistance through activating mTOR signaling in triple-negative breast cancer. Additionally, macropinocytosis, a nutrient acquisition pathway regulated by TORC1, supports cancer cell survival and metabolic reprogramming. Loss of negative regulators like GATOR1 can lead to uncontrolled proliferation.
Metabolic Liver Disease
Protein phosphatase 6 (PP6) regulates metabolic dysfunction-associated steatohepatitis via the mTORC1 pathway. Impaired PP6-mediated negative regulation of TORC1 leads to lipid accumulation and liver injury, highlighting the importance of this process in metabolic homeostasis.
Aging and Healthspan
Inhibition of IL-11 signaling extends mammalian healthspan and lifespan, potentially through modulation of mTORC1 activity. This suggests that negative regulation of TORC1 signaling is a conserved mechanism influencing aging and age-related diseases.
From negative regulation of TORC1 signaling-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of GATOR1 component cause hyperactive TORC1 signaling? | CRISPR knockout of DEPDC5, NPRL2, or NPRL3 in cell lines |
| Does a specific point mutation in PPP6C affect its phosphatase activity? | CRISPR point mutation knock-in of catalytic dead mutant |
| How does TRPML1-mediated calcium release inhibit TORC1? | Knockout and overexpression of TRPML1 in melanoma cells |
| Does GPRC5A methylation alter mTOR signaling and drug resistance? | Methylation-specific knock-in and knockout in TNBC cells |
| What is the role of IL-11 in lifespan regulation via TORC1? | IL-11 knockout mouse and overexpression models |
| How does 4F2hc/Girdin complex regulate amino acid signaling? | Knockout and tagged knock-in of Girdin in cell lines |
How to Study the negative regulation of TORC1 signaling Process
| Method | What It Measures | Typical Application |
|---|---|---|
| CRISPR knockout screening | Loss-of-function phenotypes | Identify negative regulators of TORC1 |
| Phosphoproteomics | Phosphorylation of TORC1 substrates | Quantify TORC1 activity |
| Live-cell imaging | TORC1 localization and activity dynamics | Study TRPML1-mediated inhibition |
| Ribo-seq | Translation efficiency | Assess impact on protein synthesis |
| RNA-seq | Transcriptomic changes | Evaluate gene expression programs |
| Western blot | Phosphorylation status of S6K1/4E-BP1 | Routine readout of TORC1 activity |
| Co-immunoprecipitation | Protein-protein interactions | Study GATOR1 complex assembly |
| GTPase activity assay | GAP activity toward Rag GTPases | Measure GATOR1 function |
CRISPR-Based Genetic Screens
Genome-wide CRISPR knockout or activation screens can identify novel negative regulators of TORC1 signaling. For example, screens in cancer cell lines have uncovered GATOR1 components and other modulators. These screens are powerful for discovering genes whose loss enhances or suppresses TORC1 activity.
Phosphoproteomics
Phosphoproteomic analysis of TORC1 substrates, such as S6K1 and 4E-BP1, provides a quantitative readout of TORC1 activity. By comparing wild-type and knockout cells, researchers can assess the impact of candidate negative regulators on TORC1 signaling.
Live-Cell Imaging
Live-cell imaging of TORC1 localization and activity using fluorescent reporters (e.g., GFP-tagged mTOR or FRET-based sensors) allows real-time monitoring of negative regulation. This is particularly useful for studying dynamic processes like lysosomal signaling by TRPML1.
Ribo-Seq and RNA-Seq
Ribo-seq measures translation efficiency, a direct output of TORC1 signaling. RNA-seq provides transcriptomic changes. Both can be used to evaluate how negative regulators affect global protein synthesis and gene expression programs.
How CRISPR Can Be Used to Study GO:1904262 negative regulation of TORC1 signaling
Knockout
CRISPR knockout of negative regulators such as DEPDC5, NPRL2, NPRL3, or PPP6C leads to hyperactive TORC1 signaling, providing causal evidence for their role. These models are invaluable for studying epilepsy, cancer, and metabolic diseases.
Point Mutation
Introducing disease-associated point mutations (e.g., in DEPDC5 or NPRL3) via CRISPR base editing or homology-directed repair allows researchers to dissect the functional impact of specific variants on TORC1 regulation.
Knock-in
Knock-in of tagged versions of GATOR1 components or TRPML1 enables localization and interaction studies. For example, GFP knock-in of NPRL2 can reveal its lysosomal recruitment dynamics.
Overexpression
CRISPR activation (CRISPRa) or cDNA overexpression of negative regulators like PP6 or TRPML1 can suppress TORC1 signaling, offering a way to study the consequences of enhanced inhibition.
How EDITGENE Supports negative regulation of TORC1 signaling Research
Researchers studying negative regulation of TORC1 signaling-related genes often need to determine whether a candidate gene is causally involved in the pathway or contributes to disease. EDITGENE provides a comprehensive suite of CRISPR services to accelerate this research, from generating knockout cell lines to performing high-throughput screens.
Contact EDITGENE today to design your custom CRISPR model for negative regulation of TORC1 signaling research.
Frequently Asked Questions About negative regulation of TORC1 signaling
What is GO:1904262?
GO:1904262 is the Gene Ontology term for negative regulation of TORC1 signaling, defined as any process that stops, prevents, or reduces the frequency, rate, or extent of TORC1 signaling.
What genes are involved in negative regulation of TORC1 signaling?
Key genes include DEPDC5, NPRL2, NPRL3 (GATOR1 complex), PPP6C, TRPML1, and components of the MAPK-regulated 4F2hc/Girdin complex.
How does GATOR1 inhibit TORC1?
GATOR1 acts as a GTPase-activating protein for Rag GTPases, promoting their inactive state and preventing TORC1 recruitment to the lysosome.
What diseases are associated with defective negative regulation of TORC1 signaling?
Diseases include epilepsy, cortical malformations, cancer, and metabolic dysfunction-associated steatohepatitis.
What is the role of TRPML1 in TORC1 signaling?
TRPML1, a lysosomal calcium channel, negatively regulates mTORC1 signaling and promotes protein homeostasis in melanoma cells.
How can I study negative regulation of TORC1 signaling?
Common methods include CRISPR knockout/knock-in, phosphoproteomics, Ribo-seq, and live-cell imaging.
What is the connection between IL-11 and TORC1?
Inhibition of IL-11 signaling extends healthspan and lifespan, potentially through modulation of mTORC1 activity.
What is the role of protein phosphatase 6 in TORC1 regulation?
PP6 dephosphorylates TORC1 substrates and regulates metabolic dysfunction-associated steatohepatitis via the mTORC1 pathway.
How does GPRC5A methylation affect mTOR signaling?
Methylation of GPRC5A promotes liver metastasis and docetaxel resistance through activating mTOR signaling in triple-negative breast cancer.
What CRISPR models are available for studying TORC1 negative regulators?
EDITGENE offers knockout, point mutation, knock-in, overexpression cell models, and CRISPR library screening for genes like DEPDC5, NPRL2, PPP6C, and TRPML1.
Conclusion
Negative regulation of TORC1 signaling (GO:1904262) is a critical biological process that ensures cellular growth is tightly coordinated with nutrient availability. Dysregulation of this process is linked to epilepsy, cancer, metabolic liver disease, and aging. Understanding the molecular mechanisms and key genes involved provides opportunities for therapeutic intervention. EDITGENE's CRISPR services empower researchers to dissect these pathways with precision and scale.
References
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- 3. Ou X et al.. 2024. Methylation of GPRC5A promotes liver metastasis and docetaxel resistance through activating mTOR signaling pathway in triple negative breast cancer.. Drug Resist Updat 73:101063 PMID: 38335844
- 4. Liu Z et al.. 2025. Protein phosphatase 6 regulates metabolic dysfunction-associated steatohepatitis via the mTORC1 pathway.. J Hepatol 83(3):630-642 PMID: 39947331
- 5. Weng L et al.. 2018. Negative regulation of amino acid signaling by MAPK-regulated 4F2hc/Girdin complex.. PLoS Biol 16(3):e2005090 PMID: 29538402
- 6. Bar-Peled L et al.. 2013. A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1.. Science 340(6136):1100-6 PMID: 23723238
- 7. Xu G et al.. 2025. Survival strategies of cancer cells: the role of macropinocytosis in nutrient acquisition, metabolic reprogramming, and therapeutic targeting.. Autophagy 21(4):693-718 PMID: 39817564
- 8. Kasitinon SY et al.. 2019. TRPML1 Promotes Protein Homeostasis in Melanoma Cells by Negatively Regulating MAPK and mTORC1 Signaling.. Cell Rep 28(9):2293-2305.e9 PMID: 31461647
