All About the RNA: Interferon-Stimulated Genes That Interfere With Viral RNA Processes

Abstract

Interferon (IFN) signaling induces the expression of a wide array of genes, collectively referred to as IFN-stimulated genes (ISGs) that generally function to inhibit viral replication. RNA viruses are frequently targeted by ISGs through recognition of viral replicative intermediates and molecular features associated with viral genomes, or the lack of molecular features associated with host mRNAs. The ISGs reviewed here primarily inhibit viral replication in an RNA-centric manner, working to sense, degrade, or repress expression of viral RNA. This review focuses on dissecting how these ISGs exhibit multiple antiviral mechanisms, often through use of varied co-factors, highlighting the complexity of the type I IFN response. Specifically, these ISGs can mediate antiviral effects through viral RNA degradation, viral translation inhibition, or both. While the OAS/RNase L pathway globally degrades RNA and arrests translation, ISG20 and ZAP employ targeted RNA degradation and translation inhibition to block viral replication. Meanwhile, SHFL targets translation by inhibiting -1 ribosomal frameshifting, which is required by many RNA viruses. Finally, a number of E3 ligases inhibit viral transcription, an attractive antiviral target during the lifecycle of negative-sense RNA viruses which must transcribe their genome prior to translation. Through this review, we aim to provide an updated perspective on how these ISGs work together to form a complex network of antiviral arsenals targeting viral RNA processes.

Keywords: RNA sensing; co-factors; interferon-stimulated genes; translation inhibition; viral RNA degradation.

Figure 1

Viral infection triggers the type I interferon (IFN) response. Virus entry triggers cellular pathogen sensors, which induce production of IFN and IFN regulatory factor 3 (IRF)-dependent genes. Type I IFN is secreted and binds to IFN-α receptor on the same and neighboring cells, activating production of a wider array of IFN-stimulated genes (ISGs). IRF3-dependent ISGs are colored in green. TRIMs is not inclusive of the entire TRIM family, but only those inducible by IFN.

Figure 2

ISGs inhibit RNA-centric processes in replication of RNA viruses. Upon infection, positive-sense single-stranded RNA genomes are directly translated by host machinery. Following expression of viral replicase proteins, genome replication occurs. However, negative-sense single-stranded RNA viruses bring their own RNA-dependent RNA polymerase and viral co-factors to transcribe their genomes before the viral mRNAs can be translated by host machinery for genome replication. ISGs covered in this review are shown to block global or viral translation (RNaseL, ISG20, ZAP, SHFL) and viral transcription (RBBP6, TRIMs). They can also inhibit viral replication by degrading cellular and/or viral RNA (RNase L, ISG20, ZAP). TRIMs that inhibit transcription are limited to those mentioned in this review, specifically TRIM22, TRIM25, TRIM32, and TRIM69.

Figure 3

Activation and dsRNA binding of OAS isoforms. (A) Diagram of how OAS is activated by viral dsRNA and synthesizes 2-5A to activate RNase L. Longer OAS isoforms are activated by longer dsRNA. Though all are able to synthesize 2-5A, OAS3 2-5A synthesis is necessary and sufficient for RNase L activation. RNase L exists as inactive free monomers, but dimerizes and activates upon binding to 2-5A and ATP, thereby cleaving RNA. Interestingly, IFN and some ISG transcripts are resistant to RNase L cleavage, resulting in preservation of antiviral signaling. (B) Schematic of known human OAS isoforms encoded by OAS genes OAS1, OAS2, OAS3, and OASL. Isoforms marked with * have demonstrated direct antiviral activity. Length of boxes approximates gene length, with different colored C-terminal boxes representing different coding sequences. Light blue OAS basal units are able to synthesize 2-5A, while dark blue OAS basal units are catalytically inactive. Most OAS1 isoforms are expressed by either G or A alleles, which differ by the inclusion of a G or A nucleotide at a splice acceptor site. However, OAS1 p41 and p49 have not been attributed to either G or A and are therefore labelled as “unknown.” UBL, Ubiquitin-like domain.

Figure 4

ISGs work with co-factors in varied ways to inhibit viral replication through diverse mechanisms. (A) YTHDF2 recognizes m⁶A methylation on the ϵ in HBV RNA transcripts, recruiting catalytic ISG20 to degrade HBV RNA. (B) ZAP recruits TRIM25 to ubiquitinate other host proteins, which may alter their native cellular or viral-associated activities in order to inhibit viral translation. (C) ZAP recognizes CG motifs in viral RNA and forms a complex with TRIM25 and the endonuclease KHNYN, which then putatively cleaves ZAP-bound RNA. (D) SHFL inhibits DENV replication by interacting with the viral RNA 3’UTR binding proteins PABPC1 and LARP1 and potentially inhibiting recruitment of further translation machinery.