RIG-I

DDX58
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2LWD, 2LWE, 2QFB, 2QFD, 2RMJ, 2YKG, 3LRN, 3LRR, 3NCU, 3OG8, 3ZD6, 3ZD7, 4AY2, 4BPB, 4NQK, 4ON9, 4P4H, 5E3H, 5F98, 5F9F, 5F9H
Identifiers
Aliases	DDX58, DEAD (Asp-Glu-Ala-Asp) box polypeptide 58, RIGI, RLR-1, SGMRT2, RIG-I, DEXD/H-box helicase 58, RIG1
External IDs	OMIM: 609631 MGI: 2442858 HomoloGene: 32215 GeneCards: DDX58
Gene location (Human) Chr. Chromosome 9 (human)[1] Band 9p21.1 Start 32,455,302 bp[1] End 32,526,208 bp[1]
Gene location (Mouse) Chr. Chromosome 4 (mouse)[2] Band 4|4 A5 Start 40,203,773 bp[2] End 40,239,828 bp[2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in monocyte blood Achilles tendon internal globus pallidus superficial temporal artery pericardium lymph node saphenous vein lactiferous duct gallbladder Top expressed in otolith organ utricle jejunum spleen calvaria thymus secondary oocyte submandibular gland parotid gland carotid body More reference expression data BioGPS More reference expression data
Gene ontology Molecular function nucleotide binding helicase activity zinc ion binding metal ion binding protein binding single-stranded RNA binding identical protein binding RNA binding double-stranded RNA binding double-stranded DNA binding hydrolase activity ATP binding nucleic acid binding ubiquitin protein ligase binding Cellular component cytoplasm cell projection membrane bicellular tight junction plasma membrane ruffle membrane cell junction actin cytoskeleton cytoskeleton cytosol Biological process regulation of cell migration response to exogenous dsRNA positive regulation of interferon-alpha production immune system process response to virus cytoplasmic pattern recognition receptor signaling pathway in response to virus positive regulation of gene expression positive regulation of granulocyte macrophage colony-stimulating factor production positive regulation of interleukin-8 production positive regulation of interleukin-6 production negative regulation of type I interferon production detection of virus viral process innate immune response positive regulation of transcription by RNA polymerase II RIG-I signaling pathway regulation of type III interferon production positive regulation of defense response to virus by host positive regulation of interferon-beta production protein deubiquitination positive regulation of response to cytokine stimulus cellular response to exogenous dsRNA defense response to virus positive regulation of DNA-binding transcription factor activity positive regulation of myeloid dendritic cell cytokine production Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 23586 230073 Ensembl ENSG00000107201 ENSMUSG00000040296 UniProt O95786 Q6Q899 RefSeq (mRNA) NM_014314 NM_172689 RefSeq (protein) NP_055129 NP_766277 Location (UCSC) Chr 9: 32.46 – 32.53 Mb Chr 4: 40.2 – 40.24 Mb PubMed search [3] [4]
Wikidata
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RIG-I (retinoic acid-inducible gene I) is a cytosolic pattern recognition receptor (PRR) that can mediate induction of a type-I interferon (IFN1) response.^[5] RIG-I is an essential molecule in the innate immune system for recognizing cells that have been infected with a virus. These viruses can include West Nile virus, Japanese Encephalitis virus, influenza A, Sendai virus, flavivirus, and coronaviruses.^[5][6]

RIG-I is an ATP-dependent DExD/H box RNA helicase that is activated by immunostimulatory RNAs from viruses as well as RNAs of other origins. RIG-I recognizes short double-stranded RNA (dsRNA) in the cytosol with a 5' tri- or di-phosphate end or a 5' 7-methyl guanosine (m7G) cap (cap-0), but not RNA with a 5' m7G cap having a ribose 2′-O-methyl modification (cap-1).^[7][8] These are often generated during a viral infection but can also be host-derived.^{[5][9][10][11][12]} Once activated by the dsRNA, the N-terminus caspase activation and recruitment domains (CARDs) migrate and bind with CARDs attached to mitochondrial antiviral signaling protein (MAVS) to activate the signaling pathway for IFN1.^[5][9]

Type-I IFNs have three main functions: to limit the virus from spreading to nearby cells, promote an innate immune response, including inflammatory responses, and help activate the adaptive immune system.^[13] Other studies have shown that in different microenvironments, such as in cancerous cells, RIG-I has more functions other than viral recognition.^[10] RIG-I orthologs are found in mammals, geese, ducks, some fish, and some reptiles.^[9] RIG-I is in most cells, including various innate immune system cells, and is usually in an inactive state.^[5][9] Knockout mice that have been designed to have a deleted or non-functioning RIG-I gene are not healthy and typically die embryonically. If they survive, the mice have serious developmental dysfunction.^[9] The stimulator of interferon genes STING antagonizes RIG-I by binding its N-terminus, probably as to avoid overactivation of RIG-I signaling and the associated autoimmunity.^[14]

Structure

RIG-I is encoded by the DDX58 gene in humans.^[9][15] RIG-I is a helical ATP-dependent DExD/H box RNA helicase with a repressor domain (RD) on the C-terminus that binds to the target RNA.^[5][9] Included on the N-terminus are two caspase activation and recruitment domains (CARDs) that are important for interactions with mitochondrial antiviral signaling protein (MAVS).^[5][9] RIG-I is a member of the RIG-I like receptors (RLRs) that also includes Melanoma Differentiation-Associated protein 5 (MDA5) and Laboratory of genetics physiology 2 (LGP2).^[5][9] RIG-I and MDA5 are both involved in activating MAVS and triggering an antiviral response.^[16]

Functions

As a Pattern Recognition Receptor

Pattern Recognition Receptors

Pattern Recognition Receptors (PRRs) are a part of the innate immune system used for recognizing invaders.^[17] In a viral infection, a virus enters a cell, and it takes over the cell's machinery to self replicate. Once a virus has begun replication, the infected cell is no longer useful and potentially harmful to its host, and the host's immune system must be notified. RIG-I functions as a pattern recognition receptor and PRR's are the molecules that start the notification process. PRRs recognize specific Pathogen-Associated Molecular Patterns (PAMP).^[17] Once the PAMP is recognized, it can then lead to a signaling cascade producing an inflammatory response or an interferon response. PRRs are located in many different cell types, however most notably active in the innate immune system cells. In addition, they are located in many different parts of those cells, such as the cell membrane, endosomal membrane, and in the cytosol, to provide the most protection against many types of invaders (i.e., extracellular and intracellular microbes).^[5]

RIG-I PAMPs

RIG-I is located in the cytoplasm where its function is to recognize its PAMP, which are ideally short (<300 base pairs) dsRNA with a 5′ triphosphate (5′ ppp).^[5][9] However, it has been noted that while not ideal, and response is weakened, RIG-I can recognize 5′ diphosphate (5′pp). This ability is important as many viruses have evolved to evade RIG-I, so having the dual ligand opens up more doors for recognition.^[5][9] An example of viruses evolving to evade RIG-I is in the case of certain retroviruses, such as HIV-1, encode a protease that directs RIG-I to the lysosome for degradation, and thereby evade RIG-I mediated signaling.^[6] The dsRNA can come from single-stranded RNA (ssRNA) viruses or from dsRNA viruses. The ssRNA viruses are not typically recognized as ssRNA, but through intermittent replication products in the form of dsRNA.^[5][9] RIG-I is also able to detect non-self 5′-triphosphorylated dsRNA transcribed from AT-rich dsDNA by DNA-dependent RNA polymerase III (Pol III).^[18] It is important to note, however, that the ligands of RIG-I are still being investigated and are controversial. Also notable, is that RIG-I can work together with MDA5 against viruses that RIG-I itself may not create a significant enough response.^[5][9] In addition, for many viruses, effective RIG-I-mediated antiviral responses are dependent on functionally active LGP2.^[18] Cells are synthesizing multiple types of RNA at all times, so it is important that RIG-I is not going to bind to those RNAs. Native RNA from inside the cell contains an N₁ 2'O-Methyl self RNA marker that deters RIG-I from binding.^[9][10]

Type-1 Interferon Pathway

RIG-I is a signaling molecule and is usually in a condensed resting state until it is activated. Once RIG-I is bound to its PAMP, molecules such as PACT and zinc antiviral protein short isoform (ZAPs), help keep RIG-I in an activated state which then keeps the caspase activation and recruitment domains (CARDs) ready for binding.^[5] The molecule will migrate to the mitochondrial antiviral signaling protein (MAVS) CARD domain and bind.^[5][9] RIG-I CARD interactions have their own regulatory system. Although RIG-I expresses a CARD at all times, it must be activated by the ligand before it will allow both CARDs to interact with the MAVS CARD.^[9] This interaction will start the pathway to making proinflammatory cytokines and type-1 Interferon (IFN1;IFNα and IFNβ), which create an antiviral environment.^[5][9] Once the IFN1s leave the cell, they can bind to IFN1 receptors on the cell surface from which they came from, or other cells close by.^[9] This will upregulate the production of more IFN1s, boosting an antiviral environment.^[5][9] IFN1 also activates the JAK-STAT pathway, leading to the production of IFN-stimulated genes (ISGs).^[13]

In Cancer Cells

Usually, RIG-I recognizes foreign RNA. However, it can sometimes recognize "self" RNAs. RIG-I has been shown to enable breast cancer cells (BrCa) to resist treatments and grow because of an IFN response to noncoding RNA. In contrast, RIG-I in other types of cancer, such as acute myeloid leukemia and hepatocellular carcinoma, can act as a tumor suppressor.^[10] If cancer causing viruses infect a cell, however, RIG-I can lead to cell death. Cell death can occur via apoptosis via the caspase-3 pathway, or through IFN-dependent T cells and natural killer cells.^[19]

Identification and naming

In 2000, RIG-I was named by researchers from the Shanghai Institute of Hematology who identified novel genes that respond to all-trans retinoic acid (ATRA) in leukemia cells.^[20] RIG-I and the other genes were assigned the temporary name of RIG (retinoic acid–induced gene) in the format of RIG-A, RIG-B etc by the group, however they performed no additional characterization on RIG-I.

References

Further reading

Note: RARRES3 (Gene ID: 5920) and DDX58 (Gene ID: 23586) share the RIG1/RIG-1 alias in common. RIG1 is a widely used alternative name for DExD/H-box helicase 58 (DDX58), which can be confused with the retinoic acid receptor responder 3 (RARRES3) gene, since they share the same alias. [22 Jan 2019]