RIG-I and MDA-5 Detection of Viral RNA-dependent RNA Polymerase Activity Restricts Positive-Strand RNA Virus Replication

Andrei Nikonov,Kaja Kiiver,Age Utt,Urve Toots,Rein Sikut,Mart Ustav,Tarmo Mölder,Valeria Lulla,Aleksei Lulla,Andres Merits,Andres Männik,Barbara Sherry

doi:10.1371/journal.ppat.1003610

Andrei Nikonov, Kaja Kiiver + Show 10 more

Open Access

https://doi.org/10.1371/journal.ppat.1003610

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Abstract

Type I interferons (IFN) are important for antiviral responses. Melanoma differentiation-associated gene 5 (MDA-5) and retinoic acid-induced gene I (RIG-I) proteins detect cytosolic double-stranded RNA (dsRNA) or 5′-triphosphate (5′-ppp) RNA and mediate IFN production. Cytosolic 5′-ppp RNA and dsRNA are generated during viral RNA replication and transcription by viral RNA replicases [RNA-dependent RNA polymerases (RdRp)]. Here, we show that the Semliki Forest virus (SFV) RNA replicase can induce IFN-β independently of viral RNA replication and transcription. The SFV replicase converts host cell RNA into 5′-ppp dsRNA and induces IFN-β through the RIG-I and MDA-5 pathways. Inactivation of the SFV replicase RdRp activity prevents IFN-β induction. These IFN-inducing modified host cell RNAs are abundantly produced during both wild-type SFV and its non-pathogenic mutant infection. Furthermore, in contrast to the wild-type SFV replicase a non-pathogenic mutant replicase triggers increased IFN-β production, which leads to a shutdown of virus replication. These results suggest that host cells can restrict RNA virus replication by detecting the products of unspecific viral replicase RdRp activity.

Highlights

The innate immune system is an ancient set of host defense mechanisms that utilize germline-encoded receptors for the recognition of pathogens [1]
For RNA viruses, it is believed that IFN is triggered exclusively by viral double-stranded RNA or RNA containing a 59triphosphate (59-ppp) that is produced during viral genome replication or transcription driven by viral replicases
This finding indicates that viral replicase is capable of activating the host innate immune response, deviating from the paradigm that viral nucleic acid replication or transcription must be initiated in the host cell to trigger IFN production

Summary

Introduction

The innate immune system is an ancient set of host defense mechanisms that utilize germline-encoded receptors for the recognition of pathogens [1]. This set of receptors, termed pathogen recognition receptors (PRRs), binds to the pathogen’s own structural or pathogen-induced molecules and triggers an anti-pathogenic cellular state through various signal transduction pathways. The set of molecules brought into the cells or induced by pathogens are called pathogen-associated molecular patterns (PAMPs) [2]. The presence of viral dsRNA in an animal cell is an indication of the pathogen invasion and is recognized by the innate immune system as a non-self entity, as vertebrate genomes do not encode RNA-dependent RNA polymerase (RdRp) activity. Type I IFNs and several other cytokines mediate innate immune system signals that determine the type of response elicited by the adaptive immune system [2]

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