A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells

Marques, João Trindade; Devosse, Thalie; Wang, Die; Zamanian-Daryoush, Maryam; Serbinowski, Paul; Hartmann, Rune; Fujita, Takashi; Behlke, Mark A.; Williams, Bryan R.G.

doi:10.1038/nbt1205

Cited by 340 publications

(296 citation statements)

References 28 publications

Supporting

Mentioning

279

Contrasting

Unclassified

Order By: Relevance

“…A reduction of length through progressive 3' truncation to 50 nt or less attenuated signaling in Huh7 cells (Fig. 3d), consistent with reduced RIG-I binding of short RNAs 20 . Replacement of ribocytosine with riboguannine (poly-U/UG) had no impact on PAMP signaling but progressive replacement of uridine for riboguanine to below 80% uridine or 100% polyriboguanine (poly-G) reduced or abrogated PAMP signaling, respectively, in both Huh7 cells (Fig.…”

supporting

confidence: 53%

Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA

Saito

Owen

Jiang

et al. 2008

Nature

652

732

View full text Add to dashboard Cite

Innate immune defenses are essential for the control of virus infection and are triggered through host recognition of viral macromolecular motifs known as pathogen-associated molecular patterns (PAMPs) 1. Hepatitis C virus (HCV) is an RNA virus that replicates in the liver, and infects 200 million people 2. Infection is governed by hepatic immune defenses triggered by the cellular RIG-I helicase. RIG-I binds PAMP RNA and signals IRF-3 activation to induce the expression of α/β interferon (IFN) and antiviral/interferon-stimulated genes (ISGs) that limit infection 3 -10. Here we identified the poly-uridine motif of the HCV genome 3' nontranslated region (NTR) as the PAMP substrate of RIG-I, and show that this and similar homopoly-uridine motifs present in the genome of RNA viruses is the chief feature of RIG-I recognition and immune triggering 8. 5' terminal triphosphate on the PAMP RNA was necessary but not sufficient for RIG-I binding, which was primarily dependent upon homopolymeric ribonucleotide composition, linear structure and length. The HCV PAMP RNA stimulated RIG-I-dependent signaling to induce a hepatic innate immune response in vivo, and triggered IFN and ISG expression to suppress HCV infection in vitro. These results provide a conceptual advance by identifying homopoly-uridine motfis present in the genome of HCV and other RNA viruses as the PAMP substrate of RIG-I, and define immunogenic features of the PAMP/RIG-I interaction that could be utilized as an immune adjuvant for vaccine and immunotherapy approaches.To determine the nature of the HCV PAMP RNA we conducted a functional screen to identify possible HCV PAMP RNA motifs. We assessed the ability of full length HCV genome RNA or contiguous HCV RNA segments to trigger the IFN-β promoter in transfected Huh7 cells. The full-length HCV genome RNA triggered innate immune signaling to induce the IFN-β promoter (Fig. 1a). Two regions of the HCV RNA, encoding nt 2406-3256 and nt 8872-9616, stimulated significant induction of the IFN-β promoter (Fig. 1b) with signaling activity respectively localized to nt 2406-2696 of the open reading frame and nt 9389-9619 encoding the 3' NTR (Fig.1c). Deletion of nt 9389-9619 but not nt 2408-2663 from the HCV genome significantly attenuated signaling to the IFN-β promoter (Fig 1d). PAMP motifs are typically conserved among strains of a pathogen 1 , and sequence comparison of multiple HCV genomes revealed global variability within nt 2406-3696 among virus strains but nt 9389-9616 encoded motifs of high conservation (Fig. S1) Thus, the viral 3' NTR might encode HCV PAMP motifs that trigger innate immune signaling in the host cell.The HCV 3' NTR is comprised of three regions: a variable region (VR) with potential secondary structure, a nonstructured poly-U/UC region containing polyuridine with interspersed ribocytidine, and the terminal X region containing three conserved stem-loop structures (Fig. 1e) 12 . We evaluated the ability of RNA encoding the HCV 3' NTR or each of its regions to trigger intracellular si...

show abstract

supporting

confidence: 53%

Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA

Saito

Owen

Jiang

et al. 2008

Nature

652

732

View full text Add to dashboard Cite

show abstract

“…Recent structural and biochemical analyses of RIG-I and PKR, an RNA-dependent protein kinase, revealed that additional modifications such as 5Ј triphosphate groups can play a role in the RNA recognition by RIG-I to provide additional specificity (11,12). Alternatively, VP35 can suppress host immune responses through dsRNA-independent activity perhaps by direct binding and inhibition of IRF-3 kinases (15).…”

Section: Discussionmentioning

confidence: 99%

“…Recognition of viral particles and viral RNA, including RNA modifications such as 5Ј-triphosphate (5Ј-ppp), by cytosolic pattern recognition receptor helicases RIG-I and MDA-5 leads to activation of transcription factors, including IFN regulatory factor-3 (IRF-3), IRF-7, NF-B, and AP-1 (8)(9)(10)(11)(12). These transcription factors in turn induce expression of a large number of cytokines, such as IFN-␣ and IFN-␤ (13).…”

mentioning

confidence: 99%

Structure of the Ebola VP35 interferon inhibitory domain

Leung

Ginder

Fulton

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

143

186

View full text Add to dashboard Cite

Ebola viruses (EBOVs) cause rare but highly fatal outbreaks of viral hemorrhagic fever in humans, and approved treatments for these infections are currently lacking. The Ebola VP35 protein is multifunctional, acting as a component of the viral RNA polymerase complex, a viral assembly factor, and an inhibitor of host interferon (IFN) production. Mutation of select basic residues within the C-terminal half of VP35 abrogates its dsRNA-binding activity, impairs VP35-mediated IFN antagonism, and attenuates EBOV growth in vitro and in vivo. Because VP35 contributes to viral escape from host innate immunity and is required for EBOV virulence, understanding the structural basis for VP35 dsRNA binding, which correlates with suppression of IFN activity, is of high importance. Here, we report the structure of the C-terminal VP35 IFN inhibitory domain (IID) solved to a resolution of 1.4 Å and show that VP35 IID forms a unique fold. In the structure, we identify 2 basic residue clusters, one of which is important for dsRNA binding. The dsRNA binding cluster is centered on Arg-312, a highly conserved residue required for IFN inhibition. Mutation of residues within this cluster significantly changes the surface electrostatic potential and diminishes dsRNA binding activity. The high-resolution structure and the identification of the conserved dsRNA binding residue cluster provide opportunities for antiviral therapeutic design. Our results suggest a structure-based model for dsRNA-mediated innate immune antagonism by Ebola VP35 and other similarly constructed viral antagonists.crystal structure ͉ Ebola virus ͉ RNA binding E bola viruses (EBOVs) cause severe hemorrhagic fever characterized by fever, shock, coagulation defects, and impaired immunity (1, 2). These manifestations of infection are thought to reflect subversion of the innate immune system coupled with uncontrolled viral replication, particularly in macrophages and dendritic cells (3,4). EBOV infection of these cells enhances production of proinflammatory cytokines, such as TNF-␣ and IFN (IFN)-␥, and diminishes stimulation of T cell maturation by dendritic cells (3, 4). Like other negative-strand RNA viruses that impair both innate and adaptive immunity (e.g., influenza, rabies, and measles), EBOV suppresses host IFN activities to replicate, thus resulting in serious disease (5, 6). Only individuals who survive EBOV infection show appreciable amounts of viral-specific antibodies (7), suggesting that EBOV infections lead to shutdown of early immune responses and prevent activation of adaptive immune responses.Recognition of viral particles and viral RNA, including RNA modifications such as 5Ј-triphosphate (5Ј-ppp), by cytosolic pattern recognition receptor helicases RIG-I and MDA-5 leads to activation of transcription factors, including IFN regulatory factor-3 (IRF-3), IRF-7, NF-B, and AP-1 (8-12). These transcription factors in turn induce expression of a large number of cytokines, such as IFN-␣ and IFN-␤ (13). Activated IFN genes operate in both autocrine and paracrin...

show abstract

“…Data suggesting ATP-dependent dsRNA unwinding has been reported for RIG-I (11,12), but FRET assays failed to detect strand displacement (13); there are no reports of MDA5-or LGP2-mediated helicase activity. This uncertainty regarding the ability of RLRs to function as true RNA modifying proteins evokes a question about the exact role(s) for ATP hydrolysis in their biological functions.…”

Section: Laboratory Of Genetics and Physiology 2 (mentioning

confidence: 94%

ATP Hydrolysis Enhances RNA Recognition and Antiviral Signal Transduction by the Innate Immune Sensor, Laboratory of Genetics and Physiology 2 (LGP2)

Bruns

Pollpeter

Hadizadeh

et al. 2013

Journal of Biological Chemistry

126

View full text Add to dashboard Cite

Background: Laboratory of genetics and physiology 2 (LGP2) is a cytoplasmic RNA receptor required for innate antiviral signaling. Results:LGP2 uses ATP hydrolysis to diversify RNA recognition and enhance antiviral signaling. Conclusion:LGP2 mediates antiviral responses by ATP-enhanced RNA recognition. Significance: This study reveals a novel property of LGP2 providing a mechanistic basis for its positive role in antiviral signaling.

show abstract

A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells

Cited by 340 publications

References 28 publications

Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA

Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA

Structure of the Ebola VP35 interferon inhibitory domain

ATP Hydrolysis Enhances RNA Recognition and Antiviral Signal Transduction by the Innate Immune Sensor, Laboratory of Genetics and Physiology 2 (LGP2)

Contact Info

Product

Resources

About