GO:0039552 RIG-I binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0039552 (RIG-I binding) is a molecular function describing the binding of a protein to RIG-I (also known as DDX58), a cytosolic pattern recognition receptor that initiates antiviral signaling upon viral RNA recognition.
• RIG-I binding proteins can act as positive regulators, such as IFI16, which enhances RIG-I transcription and activation to restrict influenza virus infection, or as negative regulators, such as PTENα, which blocks RIG-I activation to prevent viral inflammation.
• Regulation of RIG-I binding is critical for balancing antiviral defense and preventing immunopathology; dysregulation is linked to viral susceptibility and inflammatory diseases.
• Post-translational modifications, including ufmylation, modulate RIG-I signaling and its interactions with binding partners.
• Mitochondrial dsRNA release into the cytosol can drive inflammatory phenotypes in senescent cells, implicating RIG-I binding in aging-related inflammation.
• Experimental approaches to study RIG-I binding include knockout, point mutation, knock-in, and overexpression models, combined with RNA-seq, proteomics, and imaging.
Description
RIG-I binding (GO:0039552) is a molecular function that describes the physical interaction between a protein and RIG-I (encoded by DDX58), a cytosolic pattern recognition receptor essential for antiviral innate immunity. RIG-I detects viral RNA and triggers a signaling cascade that leads to the production of type I interferons and pro-inflammatory cytokines. Proteins that bind to RIG-I can modulate this pathway, acting as either positive or negative regulators. For example, IFI16 directly senses viral RNA and enhances RIG-I transcription and activation to restrict influenza virus infection, while PTENα blocks RIG-I activation to prevent viral inflammation. Understanding the molecular details of RIG-I binding is therefore crucial for deciphering how host cells balance effective antiviral responses with the avoidance of harmful inflammation. Researchers study RIG-I binding to identify therapeutic targets for viral infections, autoimmune diseases, and inflammatory conditions. The interaction is regulated by various mechanisms, including post-translational modifications such as ufmylation, and can be influenced by metabolic states, as seen with lactate suppressing RLR signaling by targeting MAVS. Moreover, mitochondrial dsRNA release into the cytosol can drive inflammatory phenotypes in senescent cells, highlighting the broader relevance of RIG-I binding in aging and inflammation.
RIG-I binding At A Glance
| GO ID | GO:0039552 |
|---|---|
| GO term | RIG-I binding |
| Ontology | molecular_function |
| Synonym | DDX58 binding, DDX58/RIG-I binding |
| Definition | Binding to RIG-I, a cytosolic pattern recognition receptor that initiates an antiviral signaling pathway upon binding to viral RNA. |
| Major function | Mediates protein-protein interactions that regulate RIG-I-dependent antiviral signaling. |
| Related genes | DDX58 (RIG-I), IFI16, PTEN, DHX15, MAVS, RNF125, CD97, and others. |
| Associated diseases | Viral infections, inflammatory diseases, autoimmune conditions, and senescence-associated inflammation. |
What Is GO:0039552?
According to the Gene Ontology, GO:0039552 (RIG-I binding) is defined as the binding to RIG-I, a cytosolic pattern recognition receptor that initiates an antiviral signaling pathway upon binding to viral RNA. In other words, it is the molecular function of physically interacting with the RIG-I protein, which is also known as DDX58. This binding event can regulate RIG-I activity, stability, or localization, thereby influencing downstream antiviral signaling. The term is a child of protein binding and is specific to interactions with RIG-I, distinguishing it from binding to other pattern recognition receptors.
Why Is RIG-I binding Important in Cell Biology?
RIG-I binding is a critical molecular function in innate immunity because it directly modulates the activity of RIG-I, a key sensor of viral RNA. Proteins that bind to RIG-I can either amplify or dampen antiviral signaling, and this balance is essential for effective pathogen clearance without excessive inflammation. Dysregulation of RIG-I binding has been implicated in viral pathogenesis, autoimmune disorders, and chronic inflammatory conditions. For instance, the RNA-binding protein PTENα blocks RIG-I activation to prevent viral inflammation, highlighting the importance of negative regulation. Conversely, IFI16 enhances RIG-I transcription and activation to restrict influenza virus infection, demonstrating positive regulation. Understanding the mechanisms and regulators of RIG-I binding is therefore vital for developing therapeutic strategies against infectious diseases and inflammatory disorders.
• RIG-I binding proteins are central to antiviral innate immunity, controlling the response to RNA viruses such as influenza and SARS-CoV-2.
• Dysregulated RIG-I binding can lead to excessive inflammation, contributing to autoimmune and inflammatory diseases.
• Post-translational modifications like ufmylation regulate RIG-I signaling and its interactions, offering potential therapeutic targets.
• Metabolic factors such as lactate can suppress RLR signaling by targeting MAVS, indirectly affecting RIG-I binding dynamics.
• Mitochondrial dsRNA release in senescent cells drives inflammation via RIG-I binding, linking this function to aging.
• RIG-I binding is exploited by viruses to evade immune detection, making it a target for antiviral drug development.
• Understanding RIG-I binding can inform the design of adjuvants and immunotherapies.
• Experimental models of RIG-I binding, including knockout and overexpression, are essential for dissecting its role in disease.
• RIG-I binding is a potential biomarker for interferonopathies and chronic inflammatory conditions.
• Studying RIG-I binding helps elucidate fundamental mechanisms of pattern recognition receptor regulation.
Molecular Mechanism of RIG-I binding
Recognition of Viral RNA by RIG-I
In simple terms: RIG-I acts like a security guard that spots viral RNA inside the cell.
RIG-I is a cytosolic pattern recognition receptor that binds to viral RNA, typically short double-stranded RNA with a 5' triphosphate group. Upon binding, RIG-I undergoes conformational changes that expose its CARD domains, allowing it to interact with the adaptor protein MAVS and initiate a signaling cascade. This initial recognition step is the foundation for subsequent RIG-I binding events with regulatory proteins.
Positive Regulation by Binding Partners
In simple terms: Some proteins help RIG-I do its job better by binding to it.
Several proteins enhance RIG-I activation through direct binding. For example, IFI16 directly senses viral RNA and enhances RIG-I transcription and activation to restrict influenza virus infection. This positive regulation ensures a robust antiviral response. Other positive regulators may stabilize RIG-I or promote its oligomerization, though specific mechanisms vary.
Negative Regulation by Binding Partners
In simple terms: Other proteins put the brakes on RIG-I to prevent too much inflammation.
Negative regulators bind to RIG-I and inhibit its activity or promote its degradation. PTENα, an RNA-binding protein, blocks RIG-I activation to prevent viral inflammation. Similarly, CD97 negatively regulates the innate immune response against RNA viruses by promoting RNF125-mediated RIG-I degradation. These interactions are crucial for preventing immunopathology.
Post-translational Modifications Modulating RIG-I Binding
In simple terms: Chemical tags can change how RIG-I interacts with other proteins.
Post-translational modifications such as ufmylation regulate RIG-I signaling. Ufmylation involves the attachment of ubiquitin-like protein UFM1 to target proteins, and it has been shown to regulate signaling from the RNA sensor RIG-I. Such modifications can alter RIG-I's conformation, stability, or binding affinity for partners, thereby fine-tuning the antiviral response.
Coordination with Other Signaling Molecules
In simple terms: RIG-I works together with other proteins like DHX15 and MAVS to coordinate the immune response.
DHX15 and RIG-I coordinate apoptosis and innate immune signaling by antiviral RNase L. Additionally, metabolic factors like lactate can suppress RLR signaling by targeting MAVS, indirectly affecting RIG-I binding dynamics. These interactions highlight the integration of RIG-I binding into broader cellular signaling networks.
Role in Senescence and Inflammation
In simple terms: In aging cells, RIG-I binding can trigger harmful inflammation.
Release of mitochondrial dsRNA into the cytosol is a key driver of the inflammatory phenotype of senescent cells. This dsRNA can be sensed by RIG-I, leading to activation and binding of downstream partners that promote inflammation. Thus, RIG-I binding contributes to age-related inflammatory conditions.
Key Genes Involved in GO:0039552 RIG-I binding
The following genes and proteins are key players in RIG-I binding and its regulation, as supported by published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| DDX58 (RIG-I) | Cytosolic pattern recognition receptor that binds viral RNA and initiates antiviral signaling. | Central to RIG-I binding studies; knockout and overexpression models are widely used. |
| IFI16 | Enhances RIG-I transcription and activation to restrict influenza virus infection. | Positive regulator; target for enhancing antiviral immunity. |
| PTEN | PTENα isoform blocks RIG-I activation to prevent viral inflammation. | Negative regulator; potential therapeutic target for inflammatory diseases. |
| DHX15 | Coordinates apoptosis and innate immune signaling with RIG-I via RNase L. | Modulates RIG-I-mediated apoptosis; studied in antiviral responses. |
| MAVS | Mitochondrial adaptor protein that interacts with RIG-I to propagate signaling. | Key downstream effector; targeted by lactate to suppress RLR signaling. |
| RNF125 | E3 ubiquitin ligase that promotes RIG-I degradation. | Negative regulator; involved in CD97-mediated RIG-I degradation. |
| CD97 | Negatively regulates innate immune response by promoting RNF125-mediated RIG-I degradation. | Cell surface receptor; modulates RIG-I stability. |
| UFM1 | Ubiquitin-like protein involved in ufmylation, regulating RIG-I signaling. | Post-translational modifier; affects RIG-I binding dynamics. |
| RNase L | Antiviral endoribonuclease that interacts with DHX15 and RIG-I to coordinate apoptosis. | Effector of innate immunity; links RIG-I binding to apoptosis. |
| Lactate | Metabolite that suppresses RLR signaling by targeting MAVS. | Metabolic regulator; indirectly affects RIG-I binding. |
| Mitochondrial dsRNA | Cytosolic dsRNA released from mitochondria in senescent cells. | Activates RIG-I and drives inflammation in aging. |
| NF-κB | Transcription factor activated downstream of RIG-I signaling. | Readout of RIG-I pathway activation. |
| IRF3 | Transcription factor that induces type I interferon production downstream of RIG-I. | Key effector of antiviral response. |
| Type I interferons | Cytokines produced upon RIG-I activation. | Functional outcome of RIG-I binding and signaling. |
| ISG15 | Interferon-stimulated gene product with ubiquitin-like functions. | May modulate RIG-I binding and stability. |
| ATG5 | Autophagy-related protein that can regulate RIG-I signaling. | Cross-talk between autophagy and RIG-I binding. |
| TRIM25 | E3 ubiquitin ligase that ubiquitinates RIG-I to promote signaling. | Positive regulator; enhances RIG-I binding to MAVS. |
| Riplet | E3 ubiquitin ligase that activates RIG-I. | Positive regulator; modifies RIG-I for downstream binding. |
How Is RIG-I binding Regulated?
RIG-I binding is regulated at multiple levels. Post-translational modifications, such as ufmylation, directly modulate RIG-I signaling and its interactions with partner proteins. Metabolic factors like lactate can suppress RLR signaling by targeting MAVS, indirectly affecting RIG-I binding dynamics. Additionally, the availability of viral RNA and the expression levels of binding partners such as IFI16 and PTENα influence the extent and outcome of RIG-I binding. Negative feedback mechanisms, including RNF125-mediated degradation of RIG-I, prevent sustained activation. These regulatory layers ensure a balanced antiviral response.
RIG-I binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| PTEN | Viral inflammation, autoimmunity | PTEN knockout or PTENα-specific knockout cells; overexpression of PTENα |
| IFI16 | Influenza virus infection | IFI16 knockout and overexpression in lung epithelial cells |
| CD97 | RNA virus infection, inflammation | CD97 knockout macrophages; overexpression of CD97 |
| DHX15 | Antiviral apoptosis | DHX15 knockout cells; point mutations in RNase L interaction domain |
| RIG-I (DDX58) | Broad antiviral immunity | RIG-I knockout and knock-in reporter cells; overexpression of RIG-I mutants |
Viral Infections
RIG-I binding is critical for detecting RNA viruses such as influenza and coronaviruses. Positive regulators like IFI16 enhance RIG-I activation to restrict influenza virus infection. Conversely, viruses may evade immunity by interfering with RIG-I binding or its regulators. Understanding these interactions can inform antiviral therapies.
Inflammatory and Autoimmune Diseases
Dysregulated RIG-I binding can lead to excessive inflammation. PTENα blocks RIG-I activation to prevent viral inflammation, and loss of such negative regulation may contribute to autoimmune conditions. CD97 negatively regulates the innate immune response by promoting RIG-I degradation, and its dysregulation could exacerbate inflammation.
Senescence and Aging-Related Inflammation
Release of mitochondrial dsRNA into the cytosol drives the inflammatory phenotype of senescent cells, which is sensed by RIG-I. This links RIG-I binding to age-related chronic inflammation and suggests targeting RIG-I binding as a strategy to mitigate senescence-associated pathologies.
Cancer
RIG-I binding and downstream signaling can influence tumor immunity. While direct evidence for RIG-I binding in cancer is limited, the broader RLR pathway is known to modulate antitumor immune responses. Further research is needed to establish specific roles of RIG-I binding partners in cancer.
From RIG-I binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does gene X regulate RIG-I binding? | Knockout of gene X in cell lines (e.g., HEK293T, A549) followed by co-immunoprecipitation with RIG-I. |
| Does a point mutation in RIG-I affect binding to partner Y? | Point-mutation knock-in of RIG-I in cells; compare binding affinity. |
| Does overexpression of gene Z enhance antiviral signaling? | Overexpression of gene Z in cells; measure interferon production and RIG-I binding. |
| Does a tagged RIG-I knock-in allow visualization of binding dynamics? | Tagged knock-in of RIG-I (e.g., GFP) for live-cell imaging. |
| Which genes are essential for RIG-I binding in a genome-wide screen? | CRISPR library screening with a RIG-I binding readout. |
| Does a disease-associated SNP in a binding partner alter RIG-I interaction? | Knock-in of the SNP in cells; assess binding and signaling. |
How to Study the RIG-I binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Co-immunoprecipitation | Physical interaction between RIG-I and partner proteins | Confirm known interactions; identify new binding partners |
| Mass spectrometry | Protein composition of RIG-I complexes | Discover novel RIG-I binding proteins |
| RNA-seq | Transcriptional changes downstream of RIG-I binding | Assess interferon and cytokine responses |
| Western blot | Protein levels and modifications | Validate knockout/overexpression efficiency |
| Immunofluorescence | Subcellular localization and co-localization | Visualize RIG-I binding in situ |
| CRISPR screening | Genes affecting RIG-I binding or signaling | Identify regulators in a genome-wide manner |
| Reporter assays | Activity of RIG-I-dependent promoters (e.g., IFN-β) | Measure functional impact of binding |
| Surface plasmon resonance | Binding affinity and kinetics | Quantify direct RIG-I-partner interactions |
Co-immunoprecipitation and Pull-down Assays
Co-immunoprecipitation (co-IP) is the gold standard for detecting RIG-I binding. Cells are lysed, and RIG-I is immunoprecipitated; interacting proteins are identified by Western blot or mass spectrometry. This method can confirm direct binding and identify novel partners.
Proteomics and Mass Spectrometry
Mass spectrometry-based proteomics can comprehensively identify proteins that bind to RIG-I under different conditions. This approach is useful for discovering new regulators and understanding dynamic changes in RIG-I interactomes upon viral infection.
RNA-seq and Transcriptomics
RNA sequencing can measure downstream transcriptional responses to RIG-I binding, such as interferon-stimulated genes. Comparing wild-type and knockout cells reveals the impact of specific binding partners on antiviral gene expression.
Imaging and Live-cell Analysis
Fluorescence microscopy with tagged RIG-I and binding partners allows visualization of their co-localization and dynamics in living cells. This method provides spatial and temporal insights into RIG-I binding events.
How CRISPR Can Be Used to Study GO:0039552 RIG-I binding
Knockout
CRISPR knockout of genes encoding RIG-I binding partners or RIG-I itself is used to determine their necessity in antiviral signaling. For example, knocking out IFI16 reduces RIG-I activation and increases viral susceptibility. Knockout models are essential for loss-of-function studies.
Point Mutation
Point mutations can be introduced into RIG-I or its binding partners to dissect specific interaction domains or post-translational modification sites. For instance, mutating the ufmylation site on RIG-I may alter its binding to regulators. These models provide mechanistic insights.
Knock-in
Knock-in of tagged RIG-I (e.g., GFP or HA) allows for affinity purification and imaging of RIG-I complexes in a physiological context. This approach preserves endogenous regulation and is valuable for studying dynamic binding.
Overexpression
Overexpression of RIG-I or its binding partners can amplify signaling and facilitate biochemical studies. For example, overexpressing PTENα blocks RIG-I activation and reduces inflammation. Overexpression models are useful for gain-of-function experiments.
How EDITGENE Supports RIG-I binding Research
Researchers studying RIG-I binding-related genes often need to determine whether a candidate gene is causally involved in antiviral signaling or inflammatory pathways. This requires precise genetic manipulation, which can be achieved through CRISPR-based knockout, point mutation, knock-in, or overexpression models. EDITGENE provides comprehensive services to support such studies.
Contact EDITGENE today to design your custom CRISPR model for RIG-I binding research.
Frequently Asked Questions About RIG-I binding
What is RIG-I binding?
RIG-I binding (GO:0039552) is the molecular function of physically interacting with RIG-I (DDX58), a cytosolic pattern recognition receptor that detects viral RNA and initiates antiviral signaling.
What genes are involved in RIG-I binding?
Key genes include DDX58 (RIG-I), IFI16, PTEN, DHX15, MAVS, RNF125, CD97, and UFM1, among others.
How is RIG-I binding regulated?
RIG-I binding is regulated by post-translational modifications such as ufmylation, metabolic factors like lactate, and negative feedback via RNF125-mediated degradation.
What diseases are associated with RIG-I binding?
Dysregulated RIG-I binding is linked to viral infections, inflammatory and autoimmune diseases, and senescence-associated inflammation.
What methods are used to study RIG-I binding?
Common methods include co-immunoprecipitation, mass spectrometry, RNA-seq, imaging, and CRISPR screening.
Can CRISPR be used to study RIG-I binding?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models are widely used to dissect RIG-I binding mechanisms.
What is the role of IFI16 in RIG-I binding?
IFI16 directly senses viral RNA and enhances RIG-I transcription and activation to restrict influenza virus infection.
How does PTENα affect RIG-I binding?
PTENα blocks RIG-I activation to prevent viral inflammation, acting as a negative regulator.
What is the connection between RIG-I binding and senescence?
Release of mitochondrial dsRNA into the cytosol in senescent cells activates RIG-I, driving an inflammatory phenotype.
What services does EDITGENE offer for RIG-I binding research?
EDITGENE provides knockout, point mutation, knock-in, overexpression cell models, CRISPR library screening, and bioinformatics services to study RIG-I binding and related pathways.
Conclusion
RIG-I binding (GO:0039552) is a pivotal molecular function in antiviral innate immunity, with diverse proteins modulating RIG-I activity to balance effective pathogen clearance and prevent harmful inflammation. Dysregulation of these interactions contributes to viral infections, inflammatory diseases, and aging-related pathologies. Continued research using advanced CRISPR models and high-throughput methods will further elucidate the mechanisms and therapeutic potential of targeting RIG-I binding. EDITGENE offers comprehensive services to support these investigations.
References
- 1. Yin Y et al.. 2024. RNA-binding protein PTENα blocks RIG-I activation to prevent viral inflammation.. Nat Chem Biol 20(10):1317-1328 PMID: 38773328
- 2. Ramnani B et al.. 2024. DHX15 and Rig-I Coordinate Apoptosis and Innate Immune Signaling by Antiviral RNase L.. Viruses 16(12) PMID: 39772220
- 3. Li D et al.. 2021. Pattern recognition receptors in health and diseases.. Signal Transduct Target Ther 6(1):291 PMID: 34344870
- 4. Snider DL et al.. 2022. Signaling from the RNA sensor RIG-I is regulated by ufmylation.. Proc Natl Acad Sci U S A 119(15):e2119531119 PMID: 35394863
- 5. Zhang W et al.. 2019. Lactate Is a Natural Suppressor of RLR Signaling by Targeting MAVS.. Cell 178(1):176-189.e15 PMID: 31155231
- 6. Jiang Z et al.. 2021. IFI16 directly senses viral RNA and enhances RIG-I transcription and activation to restrict influenza virus infection.. Nat Microbiol 6(7):932-945 PMID: 33986530
- 7. Chang H et al.. 2023. CD97 negatively regulates the innate immune response against RNA viruses by promoting RNF125-mediated RIG-I degradation.. Cell Mol Immunol 20(12):1457-1471 PMID: 37978243
- 8. López-Polo V et al.. 2024. Release of mitochondrial dsRNA into the cytosol is a key driver of the inflammatory phenotype of senescent cells.. Nat Commun 15(1):7378 PMID: 39191740
