Molecular Mechanisms of Innate Immune Inhibition by Non-Segmented Negative-Sense RNA Viruses

Abstract

The host innate immune system serves as the first line of defense against viral infections. Germline-encoded pattern recognition receptors detect molecular patterns associated with pathogens and activate innate immune responses. Of particular relevance to viral infections are those pattern recognition receptors that activate type I interferon responses, which establish an antiviral state. The order Mononegavirales is composed of viruses that possess single-stranded, non-segmented negative-sense (NNS) RNA genomes and are important human pathogens that consistently antagonize signaling related to type I interferon responses. NNS viruses have limited encoding capacity compared to many DNA viruses, and as a likely consequence, most open reading frames encode multifunctional viral proteins that interact with host factors in order to evade host cell defenses while promoting viral replication. In this review, we will discuss the molecular mechanisms of innate immune evasion by select NNS viruses. A greater understanding of these interactions will be critical in facilitating the development of effective therapeutics and viral countermeasures.

Keywords: Mononegavirales; innate immune evasion; interferon antagonist; viral antagonism.

Figure 1. Genome organization of NNSVs

Shown are the different viral genomes included within the Order Mononegavirales. Examples of genus and species (in parentheses) of viruses with the corresponding genome organization are listed on the right. Gene products common to all NNSVs are similarly colored, while genes unique to a specific family are different. Species abbreviations are as follows: Borna disease virus (BDV), Ebolavirus (EBOV), Nipah virus (NiV), Parainfluenza virus (PIV), respiratory syncytial virus (RSV), human metapneumovirus (MPV), rabies virus (RABV), and Midway virus (MIDWV).

Figure 2. Viral inhibitors of the type I IFN signaling pathway

A simplified representation of the type I IFN signal transduction pathway. A. IFN induction. Viral PAMPS are detected by host PRRs, such as RLRs and TLRs, which lead to the production of type I IFNs and pro-inflammatory cytokines. B. IFN response. IFNα/β binding to IFNAR1/2 activates the Jak/STAT pathway leading to the expression of ISGs. Different steps of the pathway targeted by NNSV proteins are highlighted in red.

Figure 3. PAMP sequestration by filoviral VP35 proteins

A. Crystal structure showing four molecules of Ebola virus VP35 (EBOV VP35) IID bound to an 8bp dsRNA (magenta) (PDB 3L25) [22]. The area marked with a black square is shown in greater detail in B. Residues in EBOV VP35 IID makes specific contacts to both the RNA phosphodiester backbone and the blunt ends. Residues colored blue make important protein-RNA backbone contacts while residues colored yellow contact the blunt ends. C. Crystal structure of Marburg virus VP35 (MARV VP35) IID bound to 18bp dsRNA (PDB 4GHL) showing that MARV VP35 IID does not end cap but coats the double stranded RNA backbone [23].

Figure 4. Structural rearrangement of MDA5 upon binding to the PIV5 V protein

A. Crystal structure of the SF2 domain of human MDA5 (PDB 4GL2) [127]. B. Crystal structure of the SF2 domain of porcine MDA5 (yellow) bound to PIV5 V protein residues 168 to 219 (red) (PDB 4I1S) [27]. The key interactions that stabilize the complex are shown as sticks.

Figure 5. Mechanisms of NNSV mediated inhibition of IFN induction

A. The non-structural proteins NS1 and NS2 from respiratory syncytial virus (RSV) interact with MAVS and RIG-I, respectively, to disrupt RLR signaling. B. Measles virus (MeV) V protein binds to protein phosphatase 1 α/γ (PP1α/γ) and inhibits dephosphorylation and activation of RLRs. C. Ebolavirus VP35 (EBOV VP35) protein binds to PACT and inhibits PACT-induced activation of RIG-I. D. Filoviral VP35 proteins bind to kinases TBK1 and IKKe and act as decoy substrates to inhibit the phosphorylation of IRF3/7. Paramyxoviral V protein and Bornavirus and Rhabdovirus P protein also inhibit IRF3/7 phosphorylation in a similar manner.

Figure 6. SeV C protein targets STAT1

A. Crystal structure of SeV C protein residues 99 to 204 bound to human STAT1 N-terminal domains (residues 1–126) (PDB 3WWT) [70]. B. Expanded view of a key electrostatic interaction between SeV C protein residue Arg154 and STAT1 residue His58, which highlights the role of charge complementarity at the host-viral interface. C. Expanded view of a hydrophobic pocket. SeV C residue Met150 inserts into the hydrophobic pocket within STAT1.

Figure 7. Inhibition of the JAK/STAT pathway by EBOV VP24

A. Crystal structure of EBOV VP24 (red) in complex with ARM 7–10 of KPNA5 (dark blue) (PDB 4U2X) [76]. ARM 7–10 is aligned to the structure of full length KPNA (cyan) (PDB 1BK5) [77] as reference. B. Model showing how EBOV VP24 targets the non-classical nuclear localization signal (ncNLS) recognition of KPNA and blocks nuclear accumulation of pY-STAT1 while leaving classical NLS interactions intact.

Figure 8. Viral modulation of host ubiquitination

[70] A. Cartoon model depicting the mechanism of SV5 V protein mediated ubiquitination of STAT2. B. Crystal structure of the complex of SV5 V protein (red), DDB1 (green), Cullin4 (grey), and Rbx1 (Blue) (PDB 2HYE) [118]. BPB of DDB1 binds to the N-terminal domain of Cullin4, while Rbx1 binds to the C-terminal domain of Cullin4. C. Crystal structure of Simian virus 5 (SV5) V protein (red) and DDB1 (green) showing the three β-propellers BPA, BPB, and BPC (PDB 2B5l) [117]. The SV5 V protein binds at a pocket within the BPA and BPC. D. Close up of the V binding pocket. N-terminal helix α1 of V protein inserts into the hydrophobic pocket of DDB1. Tyr127 of V protein makes important inter-subunit interactions with BPC.