Strategies of highly pathogenic RNA viruses to block dsRNA detection by RIG-I-like receptors: hide, mask, hit

Abstract

Double-stranded RNA (dsRNA) is synthesized during the course of infection by RNA viruses as a byproduct of replication and transcription and acts as a potent trigger of the host innate antiviral response. In the cytoplasm of the infected cell, recognition of the presence of viral dsRNA as a signature of "non-self" nucleic acid is carried out by RIG-I-like receptors (RLRs), a set of dedicated helicases whose activation leads to the production of type I interferon α/β (IFN-α/β). To overcome the innate antiviral response, RNA viruses encode suppressors of IFN-α/β induction, which block RLRs recognition of dsRNA by means of different mechanisms that can be categorized into: (i) dsRNA binding and/or shielding ("hide"), (ii) dsRNA termini processing ("mask") and (iii) direct interaction with components of the RLRs pathway ("hit"). In light of recent functional, biochemical and structural findings, we review the inhibition mechanisms of RLRs recognition of dsRNA displayed by a number of highly pathogenic RNA viruses with different disease phenotypes such as haemorrhagic fever (Ebola, Marburg, Lassa fever, Lujo, Machupo, Junin, Guanarito, Crimean-Congo, Rift Valley fever, dengue), severe respiratory disease (influenza, SARS, Hendra, Hantaan, Sin Nombre, Andes) and encephalitis (Nipah, West Nile).

Keywords: Innate immune system evasion; Interferon alpha/beta; LGP2; MDA5; RIG-I; Viral dsRNA detection.

Fig. 1

Schematic representation of RLR-mediated type I IFN induction and viral strategies aimed at its suppression. Recognition of viral dsRNA by RLRs leads to the production of type I IFN-α/β, triggering an innate immune antiviral response. Viruses prevent it by processing dsRNA (Mask), sequestering dsRNA (Hide) or physically interacting with the host proteins involved in the RLRs pathway (Hit).

Fig. 2

Structural organization of RLRs. RIG-I, MDA5 and LGP2 share an overall domain organization that consists of two tandemly-repeated N-terminal CARDs (orange boxes, absent in LGP2) followed by an Hel domain (green box in RIG-I and MDA5, blue box in LGP2) and a C-terminal RNA binding CTD (violet, azure and cyan box in RIG-I, MDA5 and LGP2 respectively).

Fig. 3

Activation of the type I IFN antiviral response triggered by the RLRs pathway upon dsRNA detection. Viral short 5′-ppp dsRNA and long dsRNA are preferentially recognized by the CTD of RIG-I (violet) and of MDA5 (azure) respectively, with LGP2 modulating the activity of RIG-I helicase. Upon dsRNA binding to their Hel domain (green), ATP-mediated homo-oligomerization, translocation onto dsRNA, ubiquitination, and TRIM25- or Riplet-mediated ubiquitination, RLRs interact through their CARDs (orange) with the CARD of mitochondrion-associated MAVS (red). Signaling prosecution involves recruitment of TRAF3, NEMO and STING adaptors and the assembly of TBK1-IKK-ε complex, which phosphorylates IRFs. Activated IRF dimers translocate to the nucleus and, together with other transcription factors, induce the expression of IFN-α/β. Type I IFNs are secreted and bind to their cognate receptor, activating STAT transcription factors for the induction of several ISG products with antiviral activity and the overexpression of RLRs pathway components.

Fig. 4

Hide and Mask strategies. Production of type I IFN-α/β is prevented by keeping RLRs from being triggered by short 5′-ppp dsRNA and long dsRNA molecules. (A) In the Hide strategy, nucleic acids are (i) bound by viral IFN-antagonists that compete with RLRs for the same binding sites on dsRNA backbone and/or terminal bases and phosphate groups; (ii) sequestered from RLRs recognition by compartmentalization into virally–assembled CMs and DMVs. (B) In the Mask strategy, viral IFN-antagonists remove PAMP signatures from dsRNA by (i) processing terminal 5′-ppp to monophosphate groups; (ii) digesting one nucleic acid strand through exoribonuclease activity.

Fig. 5

Hit strategy. In the Hit strategy, viral IFN antagonists suppress RLRs-mediated IFN-α/β induction by interacting with RLRs and their adaptor and/or effector molecules to inhibit their functionalities.

Fig. 6

Structures of viral proteins dispaying the Mask and the Hit strategies. (A) LASFV NP masks dsRNA: LASFV may evade host cell dsRNA-induced innate immune antiviral response through the 3′–5′ exoribonuclease activity of its NP protein (highlighted in deep olive, PyMOL colors), which eliminates 5′-ppp and double-strandness PAMP signatures from viral dsRNA. Crystallographic structure by Jiang et al., 2013 (PDB: 4G9Z); (B) CCHFV vOTU hits human Ubiquitin: CCHFV may downregulate RLRs pathway-mediated type I IFN production through the activity of its vOTU protease (highlighted in deep salmon, PyMOL colors), which removes ubiquitin (highlighted in gray, PyMOL colors) from RLRs, their adaptor and/or effector molecules, impairing their proper signaling. Crystallographic structure by Capodagli et al., 2011 (PDB: 3PRP); (C) Paramyxovirus V hits MDA5: HeV and NiV inhibit RLRs pathway-mediated IFN-α/β induction by preventing MDA5 activation and signaling through its sequestration by V protein. As shown in figure for the henipavirus closely-related PIV5, V protein zinc finger domain (highlighted in violet–purple, PyMOL colors) interacts with the Hel2 domain of MDA5 (highlighted in olive, PyMOL colors), thereby inhibiting its ATPase activity. Crystallographic structure by Motz et al., 2013 (PDB: 4I1S).

Fig. 7

Structures of viral proteins displaying the Hide strategy. (A) EBOV VP35 hides dsRNA: EBOV suppresses IFN-α/β production through the properties of its VP35 protein, which sequesters dsRNA from RLRs detection. VP35 RBD shields RLRs recognition sites on a 8 bp dsRNA binding to its phosphate backbone (backbone-binding monomers, highlighted in gray, PyMOL colors) and to its terminal bases and phosphate groups (end-capping monomers, highlighted in light teal, PyMOL colors). Crystallographic structure by Leung et al., 2010a, Leung et al., 2010b (PDB: 3L25); (B) MARV VP35 hides dsRNA: MARV VP35 RBD monomers fully coat a 12 bp dsRNA molecule along to its phosphate backbone. Crystallographic structure by Bale et al., 2012 (PDB: 4GHA); (C) IAV NS1 hides dsRNA: IAVs suppress type I IFN-based innate immune response through the properties of the multifunctional NS1 protein. The NS1 RBD dimer (highlighted in sky blue and light blue, PyMOL colors) coats dsRNA along to its phosphate backbone, thereby preventing its recognition by RLRs and PKR. Crystallographic structure by Cheng et al., 2009 (PDB: 2ZKO).