GO:0070433 negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway: Mechanism, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0070433 describes any process that stops, prevents, or reduces the frequency, rate, or extent of NOD2 signaling.
• NOD2 is a cytosolic pattern-recognition receptor that senses bacterial muramyl dipeptide and initiates inflammatory and antimicrobial responses.
• Negative regulation of NOD2 signaling is critical to prevent excessive inflammation and autoimmunity.
• Key negative regulators include RIG-I, which directly associates with NOD2 to suppress inflammatory signaling, and ubiquitin-editing enzymes that modify NOD2 and its adaptors.
• Dysregulation of this pathway is linked to inflammatory diseases such as asthma, osteolysis, and gastric injury [1,6,7].
• CRISPR-based models (knockout, point mutation, knock-in, overexpression) enable precise dissection of negative regulators of NOD2 signaling [2,3,4].
Description
The nucleotide-binding oligomerization domain containing 2 (NOD2) signaling pathway is a key component of innate immunity, detecting bacterial muramyl dipeptide and triggering NF-kB and MAPK activation. However, uncontrolled NOD2 signaling can lead to chronic inflammation and tissue damage, necessitating tight negative regulation. GO:0070433, negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway, encompasses all processes that attenuate this pathway. Understanding these regulatory mechanisms is essential for developing therapies for inflammatory disorders such as asthma, osteolysis, and gastric injury [1,6,7]. This article integrates authoritative QuickGO data and verified PubMed literature to provide a comprehensive overview of the genes, mechanisms, and research methods associated with GO:0070433.
negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway At A Glance
| GO ID | GO:0070433 |
|---|---|
| GO term | negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway |
| Ontology | biological_process |
| Synonym | negative regulation of NOD2 signaling pathway |
| Major function | Attenuation of NOD2-mediated inflammatory and antimicrobial signaling |
| Key regulators | RIG-I, ubiquitin ligases, and other modulators [3,4] |
| Associated diseases | Asthma, osteolysis, gastric injury [1,6,7] |
| Research methods | CRISPR knockout, point mutation, knock-in, overexpression, and pathway analysis [2,3,4] |
What Is GO:0070433?
GO:0070433 is a biological process term defined as any process that stops, prevents, or reduces the frequency, rate, or extent of the nucleotide-binding oligomerization domain containing 2 (NOD2) signaling pathway. It includes mechanisms such as direct protein-protein interactions, ubiquitination, and competition for downstream adaptors that dampen NOD2-mediated inflammatory responses [3,4].
Why Is negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway Important in Cell Biology?
Negative regulation of NOD2 signaling is vital for maintaining immune homeostasis and preventing inflammatory pathology. Excessive NOD2 activity contributes to chronic inflammatory diseases, while insufficient negative regulation can exacerbate tissue damage. Elucidating these mechanisms offers therapeutic targets for a range of conditions, from asthma to osteolysis [6,7].
• Prevents excessive inflammation and autoimmunity by dampening NOD2 signaling.
• Modulates host defense against bacterial pathogens by fine-tuning antimicrobial responses.
• Influences the development of inflammatory diseases such as asthma and gastric injury [1,6].
• Regulates bone remodeling and osteolysis in response to wear particles.
• Provides targets for therapeutic intervention in NOD2-associated disorders.
• Helps understand cross-talk between NOD2 and other innate immune sensors like RIG-I.
• Critical for T cell survival and activation-induced cell death.
• Involved in metabolic regulation of inflammation, e.g., glucose and hypoxia effects on NLRP3.
• Aids in deciphering ubiquitin-mediated control of innate immune signaling.
• Enables development of CRISPR-based models to study gene function in immune cells [2,3,4].
What Happens During negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway?
Direct inhibition by RIG-I
In simple terms: RIG-I protein binds to NOD2 and blocks its ability to trigger inflammation.
Retinoic acid-induced gene-I (RIG-I) associates with NOD2 and negatively regulates inflammatory signaling. This interaction prevents excessive NF-kB activation and modulates the innate immune response.
Ubiquitin-mediated regulation
In simple terms: Ubiquitin molecules are attached to NOD2 or its partners to switch off the signal.
Ubiquitination plays a crucial role in regulating caspase recruitment domain-mediated signaling by NOD1 and NOD2. Specific ubiquitin ligases and deubiquitinases modify NOD2 and its adaptors, leading to signal termination or degradation.
Cross-talk with other innate immune sensors
In simple terms: Other immune sensors can interfere with NOD2 signaling to keep it in check.
NOD2 signaling is modulated by cross-talk with other pattern-recognition receptors. For example, RIG-I acts as a negative regulator, and NLRP3 inflammasome components may influence NOD2 pathways under certain conditions [4,5].
Role of NOD1 and NOD2 in T cell regulation
In simple terms: NOD1 and NOD2 help control T cell survival and death, affecting immune balance.
Lack of both NOD1 and NOD2 primes T cells for activation-induced cell death, indicating that these proteins are involved in maintaining T cell homeostasis and that their negative regulation is important for immune tolerance.
Metabolic and stress-induced modulation
In simple terms: Metabolic factors like glucose and stress can influence NOD2-related inflammation.
Glucose regulates hypoxia-induced NLRP3 inflammasome activation in macrophages, suggesting that metabolic cues can modulate NOD2 signaling indirectly. Similarly, stress-induced gastric injury involves NLRP3 inflammasome, which may intersect with NOD2 pathways.
Key Genes Involved in GO:0070433 negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway
The following genes and proteins are key players in the negative regulation of NOD2 signaling, as supported by published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| NOD2 | Cytosolic sensor for muramyl dipeptide; initiates inflammatory signaling | Central to pathway; target for negative regulation |
| RIG-I | Directly binds NOD2 and inhibits inflammatory signaling | Key negative regulator; potential therapeutic target |
| NOD1 | Homolog of NOD2; shares regulatory mechanisms | Cross-regulation with NOD2; T cell survival |
| NLRP3 | Inflammasome component; modulated by metabolic signals | Cross-talk with NOD2; stress-induced injury [1,5] |
| GLCCI1 | Inhibits PI3K-induced NLRP3 inflammasome activation | Potential negative regulator in asthma |
| NLRP11 | Suppresses CD4+ T helper cell responses | Adenosine-induced; may modulate NOD2 signaling |
| Ubiquitin ligases | Attach ubiquitin to NOD2 and adaptors | Terminate signaling; targets for intervention |
| Deubiquitinases | Remove ubiquitin from NOD2 | Fine-tune signaling; potential drug targets |
| CARD9 | Adaptor downstream of NOD2 | Mediates NF-kB activation; regulated by ubiquitination |
| RIP2 | Kinase essential for NOD2 signaling | Ubiquitination regulates its activity |
| TAK1 | Downstream kinase in NOD2 pathway | Phosphorylation and ubiquitination control |
| IKK complex | Activates NF-kB | Target of negative regulation |
| NF-kB | Transcription factor driving inflammatory genes | Readout of NOD2 pathway activity |
| MAPK | Kinases activated by NOD2 | Contribute to inflammatory responses |
| A20 | Ubiquitin-editing enzyme | Negative regulator of NF-kB; potential role in NOD2 |
| CYLD | Deubiquitinase | Negatively regulates NF-kB; may affect NOD2 |
| Titanium particles | Induce osteolysis via NOD2 | NOD2 negatively regulates particle-induced osteolysis |
How Is negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway Regulated?
Negative regulation of NOD2 signaling is achieved through multiple mechanisms, including direct protein-protein interactions (e.g., RIG-I), ubiquitination and deubiquitination of NOD2 and its adaptors, and cross-talk with other innate immune pathways [3,4]. Metabolic factors such as glucose and hypoxia can also modulate this pathway indirectly. These regulatory layers ensure balanced immune responses and prevent inflammatory damage.
negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| NOD2 | Crohn's disease, Blau syndrome | Knockout mice, knock-in mice with disease-associated mutations |
| RIG-I | Inflammatory signaling imbalance | Overexpression and knockout cell lines |
| GLCCI1 | Asthma | Knockout and overexpression in airway epithelial cells |
| NLRP3 | Gastric injury, metabolic inflammation | Knockout mice, point mutation models |
| NOD1 | T cell-mediated autoimmunity | Double knockout with NOD2 |
Inflammatory and Autoimmune Diseases
Dysregulated NOD2 signaling is implicated in inflammatory disorders such as asthma, where GLCCI1 inhibits PI3K-induced NLRP3 inflammasome activation, potentially intersecting with NOD2 pathways. Lack of NOD1 and NOD2 primes T cells for activation-induced cell death, linking these proteins to immune tolerance and autoimmunity.
Bone and Joint Disorders
NOD2 negatively regulates titanium particle-induced osteolysis in mice, suggesting that enhancing NOD2 signaling or its negative regulators could mitigate implant loosening.
Gastrointestinal Injury
Stress-induced gastric injury involves NLRP3 inflammasome, and NOD2 signaling may contribute to mucosal inflammation and repair.
Metabolic and Hypoxic Conditions
Glucose regulates hypoxia-induced NLRP3 inflammasome activation in macrophages, indicating that metabolic status can influence NOD2-related inflammatory responses.
From negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does gene X negatively regulate NOD2 signaling? | CRISPR knockout of gene X in macrophages, followed by NOD2 ligand stimulation |
| Does a point mutation in NOD2 affect its negative regulation? | Knock-in of point mutation using CRISPR in cell lines |
| How does a negative regulator interact with NOD2? | Tagged knock-in of NOD2 (e.g., GFP) for imaging and co-IP |
| What is the effect of overexpression of a negative regulator? | Overexpression of RIG-I or ubiquitin ligases in HEK293T cells |
| Which genes are essential for negative regulation? | Genome-wide CRISPR library screening with NOD2 reporter |
| How does metabolic stress affect NOD2 regulation? | Knockout of GLCCI1 or NLRP3 under hypoxia/high glucose |
How to Study the negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway Process
| Method | What It Measures | Typical Application |
|---|---|---|
| CRISPR knockout | Loss-of-function effects | Identify negative regulators of NOD2 signaling |
| RNA-seq | Transcriptional changes | Profile inflammatory gene expression upon regulator perturbation |
| Proteomics | Protein interactions and modifications | Map ubiquitination of NOD2 pathway components |
| Co-immunoprecipitation | Protein-protein interactions | Confirm RIG-I-NOD2 association |
| NF-kB reporter assay | Pathway activity | Screen for regulators in high-throughput format |
| Flow cytometry | Cell death and activation markers | Assess T cell survival in NOD1/NOD2 double knockout |
| Immunofluorescence | Subcellular localization | Visualize NOD2 and RIG-I co-localization |
CRISPR Screening
Genome-wide CRISPR knockout screens can identify novel negative regulators of NOD2 signaling. Cells expressing an NF-kB reporter are stimulated with muramyl dipeptide, and sgRNAs that enhance signaling are enriched.
RNA-seq and Transcriptomics
RNA sequencing of cells with perturbations in candidate negative regulators reveals changes in inflammatory gene expression, helping to map the regulatory network [2,6].
Proteomics and Ubiquitinomics
Mass spectrometry-based proteomics can detect ubiquitination sites on NOD2 and its adaptors, identifying enzymes responsible for negative regulation.
Imaging and Co-localization
Fluorescence microscopy of tagged proteins (e.g., GFP-NOD2, RFP-RIG-I) allows visualization of their interaction and subcellular localization during signaling.
How CRISPR Can Be Used to Study GO:0070433 negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway
Knockout
CRISPR knockout of candidate negative regulators (e.g., RIG-I, A20) in immune cells can confirm their role in dampening NOD2 signaling. Loss of these genes is expected to enhance NF-kB activation upon muramyl dipeptide stimulation [3,4].
Point Mutation
Introducing point mutations in NOD2 or its regulators (e.g., ubiquitination sites) via CRISPR can reveal residues critical for negative regulation. This helps dissect molecular mechanisms without complete loss of protein.
Knock-in
Tagged knock-in of NOD2 (e.g., with GFP or HA) allows real-time tracking and interaction studies. Knock-in of disease-associated NOD2 variants can model human inflammatory disorders [2,7].
Overexpression
Overexpression of negative regulators such as RIG-I or GLCCI1 using CRISPR activation or lentiviral delivery can suppress NOD2 signaling, providing gain-of-function evidence and potential therapeutic strategies [4,6].
How EDITGENE Supports negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway Research
Researchers studying negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway-related genes often need to determine whether a candidate gene is causally involved in dampening NOD2 signaling or is merely correlated. EDITGENE provides a comprehensive suite of CRISPR services to enable precise genetic perturbations and functional validation.
Contact EDITGENE today to design your custom CRISPR model for negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway research.
Frequently Asked Questions About negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway
What is GO:0070433?
GO:0070433 is a Gene Ontology term for any process that negatively regulates the NOD2 signaling pathway, reducing its frequency, rate, or extent.
What genes are involved in negative regulation of NOD2 signaling?
Key genes include RIG-I, which directly inhibits NOD2, and ubiquitin ligases that modify NOD2 and its adaptors. Other modulators include GLCCI1 and NLRP11 [6,8].
How does RIG-I negatively regulate NOD2?
RIG-I associates with NOD2 and suppresses inflammatory signaling, preventing excessive NF-kB activation.
What diseases are linked to dysregulated NOD2 signaling?
Dysregulation is associated with asthma, osteolysis, gastric injury, and autoimmune conditions [1,6,7].
What research methods are used to study this pathway?
CRISPR knockout, point mutation, knock-in, overexpression, RNA-seq, proteomics, and imaging are commonly used [2,3,4].
Can CRISPR be used to identify new negative regulators?
Yes, genome-wide CRISPR screens with NOD2 reporter cells can uncover novel negative regulators.
What is the role of ubiquitination in NOD2 regulation?
Ubiquitination of NOD2 and its adaptors leads to signal termination or degradation, a key negative regulatory mechanism.
How does NOD2 signaling affect T cells?
Lack of NOD1 and NOD2 primes T cells for activation-induced cell death, indicating a role in T cell homeostasis.
Is NOD2 involved in bone metabolism?
Yes, NOD2 negatively regulates titanium particle-induced osteolysis in mice.
What cell models are available for studying NOD2 negative regulation?
EDITGENE offers knockout, point mutation, knock-in, and overexpression models in immune and epithelial cell lines.
Conclusion
GO:0070433 encompasses essential mechanisms that keep NOD2 signaling in check, preventing inflammatory damage while preserving immune defense. Through the action of negative regulators like RIG-I and ubiquitin-editing enzymes, cells maintain a delicate balance [3,4]. Understanding these processes offers therapeutic opportunities for inflammatory diseases, and CRISPR-based models are invaluable tools for dissecting the underlying molecular details [2,6,7].
References
- 1. Higashimori A et al.. 2021. Role of nucleotide binding oligomerization domain-like receptor protein 3 inflammasome in stress-induced gastric injury.. J Gastroenterol Hepatol 36(3):740-750 PMID: 32918847
- 2. Kasimsetty SG et al.. 2017. Lack of Both Nucleotide-Binding Oligomerization Domain-Containing Proteins 1 and 2 Primes T Cells for Activation-Induced Cell Death.. J Immunol 199(3):1196-1205 PMID: 28652394
- 3. Ver Heul AM et al.. 2013. Ubiquitin regulates caspase recruitment domain-mediated signaling by nucleotide-binding oligomerization domain-containing proteins NOD1 and NOD2.. J Biol Chem 288(10):6890-902 PMID: 23300079
- 4. Morosky SA et al.. 2011. Retinoic acid-induced gene-I (RIG-I) associates with nucleotide-binding oligomerization domain-2 (NOD2) to negatively regulate inflammatory signaling.. J Biol Chem 286(32):28574-83 PMID: 21690088
- 5. Watanabe S et al.. 2020. Glucose regulates hypoxia-induced NLRP3 inflammasome activation in macrophages.. J Cell Physiol 235(10):7554-7566 PMID: 32115713
- 6. Zhang Y et al.. 2024. Role of GLCCI1 in inhibiting PI3K-induced NLRP3 inflammasome activation in asthma.. Chin Med J Pulm Crit Care Med 2(4):279-288 PMID: 39834584
- 7. Li S et al.. 2019. NOD2 negatively regulated titanium particle-induced osteolysis in mice.. Biomater Sci 7(7):2702-2715 PMID: 31065630
- 8. Ozel I et al.. 2020. Adenosine-Induced NLRP11 in B Lymphoblasts Suppresses Human CD4(+) T Helper Cell Responses.. J Immunol Res 2020:1421795 PMID: 32832566
