RNA regulatory processes in RNA virus biology

Abstract

Numerous post-transcriptional RNA processes play a major role in regulating the quantity, quality and diversity of gene expression in the cell. These include RNA processing events such as capping, splicing, polyadenylation and modification, but also aspects such as RNA localization, decay, translation, and non-coding RNA-associated regulation. The interface between the transcripts of RNA viruses and the various RNA regulatory processes in the cell, therefore, has high potential to significantly impact virus gene expression, regulation, cytopathology and pathogenesis. Furthermore, understanding RNA biology from the perspective of an RNA virus can shed considerable light on the broad impact of these post-transcriptional processes in cell biology. Thus the goal of this article is to provide an overview of the richness of cellular RNA biology and how RNA viruses use, usurp and/or avoid the associated machinery to impact the outcome of infection. This article is categorized under: RNA in Disease and Development > RNA in Disease.

Keywords: RNA decay; RNA export; RNA methylation; RNA virus; RNA virus-host interactions; capping; non-coding RNAs; polyadenylation; splicing; translation; virus.

Figure 1

RNA viruses can use and/or usurp cellular RNA splicing during infection. Panel a. Two segments of influenza A viral RNA are processed by the cellular RNA splicing machinery to increase the coding capacity of viral genome. Illustrated here is segment 7 which can generate mRNAs that remain unspliced to provide a transcript to generate the viral M1 protein or can be alternatively spliced to yield several other products, including mRNAs to generate the M2 and M42 proteins as illustrated here. Panel b. While no transcripts of the cytoplasmic reoviruses are directly spliced by the cellular machinery, the reovirus T1L strain does generate the μ2 protein which sequesters the alternative splicing factor SRSF2 in nuclear speckles and causes dysregulation of cellular mRNA splicing

Figure 2

Three major approaches used by RNA viruses to generate the 3′ ends of viral mRNAs. Panel a. Template‐dependent poly(A) formation. Some viruses (e.g., picornaviruses) possess a poly(U) stretch at the 5′ end of their negative strand RNA template that can be directly copied by the viral RdRp to generate a poly(A) tail on the viral mRNAs. Panel b. Reliance on a stuttering RdRp to generate a poly(A) tail. Some viruses (e.g., rhabdoviruses) contain short U‐rich tracts near the 5′ end of genes on the negative sense strand that serves a slippery site for the viral RdRp to stutter upon, thus generating a poly(A) tail on the positive‐sense mRNA product. Panel c. Termination with a large structure at the 3′ end precludes the need for a poly(A) tail. Finally, other viruses (e.g., flaviviruses) have a large hairpin structure at their 3′ end which serves the purpose of a poly(A) tail to protect the RNAs from 3′‐5′ exonucleases as well as promote translation

Figure 3

RNA editing of RNA virus transcripts. Panel a. Select mRNAs generated by paramyxoviruses and filoviruses can contain an additional one to ~8 G residues due to slippage/stuttering of the viral RdRp in certain regions during transcription. Panel b. The cell possesses inducible RNA deaminases such as ADAR that can deaminate adenosine residues to inosines. These enzymes can increase the mutation rate of RNA viruses and thus can affect viral fitness and evolution

Figure 4

An overview of HCV IRES‐dependent translation. The HCV IRES is a classified as “Type III” and recruits a preinitiation complex (PIC) that includes eIF1, eIF1A, and eIF3. Binding to the HCV IRES causes displacement of eIF1. Translation initiation then proceeds by one of two pathways depending on the state (active or inactive) of eIF2 in the cell. For more information, see the accompanying text in section 8.1

Figure 5

Major approaches used by RNA viruses to confound the cellular RNA decay machinery. RNA viruses effectively subvert the cellular RNA decay machinery by a variety of mechanisms. Top Panel: RNA‐mediated mechanisms include the use of high affinity binding sites to sequester and usurp cellular RNA stabilizing factors (e.g., alphaviruses) as well as the use of complex RNA structures to prevent binding or repress RNA exonucleases (e.g., flaviviruses). Bottom Panel: RNA viruses (e.g., polioviruses) can also encode proteases that can selectively cleave cellular factors involved in RNA decay. Alternatively RNA viruses like coronaviruses encode nonstructural proteins that facilitate massive degradation of cellular RNA that somehow gives viral RNAs a competitive advantage

Figure 6

Examples of mechanisms RNA viruses use to suppress RNA interference. RNA viruses target various components of the host cell RNAi machinery as part of the molecular arms race to effectively establish infection. Double‐stranded RNA (dsRNA) is sequestered (e.g., by Ebola VP35 or Influenza A virus NS1) or degraded (e.g., by virally‐encoded RNase III‐like enzymes) to inhibit the RNAi machinery from detecting this key substrate. Cellular enzymes like dicer or argonaute are bound and repressed by viral proteins (e.g., Ebola VP30 or Dengue virus NS4B) or viral RNAs (e.g., flavivirus sfRNA). Finally, DENV NS3 protein interacts with hsc70, impacting the assembly of the RISC effector complex

Figure 7

Sponging of cellular factors by RNA virus transcripts. Panel a: Sponging of cellular miRNAs by members of the Flaviviridae. HCV uses sequences in its 5’ UTR to sponge miR‐122 while bovine viral diarrhea virus and other pestiviruses use 3’ UTR sequences to sponge miR‐17. In both cases, miR sponging increases viral RNA stability while dysregulating aspects of cellular gene expression normally influenced by the small RNAs. Panel b: Insect‐borne flaviviruses contain a knot‐like structure in the 3’ UTR region of their mRNA that generates a stable RNA decay intermediate called sfRNA. The sfRNA not only effectively represses the exoribonuclease that generates it due to slow release of the stalled enzyme, but also sponges key proteins involved in the RNA interference and interferon pathways, resulting in the repression of these key aspects of cellular anti‐viral defense