The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis

Abstract

The Flavivirus genus comprises many viruses (including dengue, Zika, West Nile and yellow fever viruses) which constitute important public health concerns worldwide. For several of these pathogens, neither antivirals nor vaccines are currently available. In addition to this unmet medical need, flaviviruses are of particular interest since they constitute an excellent model for the study of spatiotemporal regulation of RNA metabolism. Indeed, with no DNA intermediate or nuclear step, the flaviviral life cycle entirely relies on the cytoplasmic fate of a single RNA species, namely the genomic viral RNA (vRNA) which contains all the genetic information necessary for optimal viral replication. From a single open reading frame, the vRNA encodes a polyprotein which is processed to generate the mature viral proteins. In addition to coding for the viral polyprotein, the vRNA serves as a template for RNA synthesis and is also selectively packaged into newly assembled viral particles. Notably, vRNA translation, replication and encapsidation must be tightly coordinated in time and space via a fine-tuned equilibrium as these processes cannot occur simultaneously and hence, are mutually exclusive. As such, these dynamic processes involve several vRNA secondary and tertiary structures as well as RNA modifications. Finally, the vRNA can be detected as a foreign molecule by cytosolic sensors which trigger upon activation antiviral signaling pathways and the production of antiviral factors such as interferons and interferon-stimulated genes. However, to create an environment favorable to infection, flaviviruses have evolved mechanisms to dampen these antiviral processes, notably through the production of a specific vRNA degradation product termed subgenomic flavivirus RNA (sfRNA). In this review, we discuss the current understanding of the fates of flavivirus vRNA and how this is regulated at the molecular level to achieve an optimal replication within infected cells.

Keywords: RNA encapsidation; West Nile virus; Zika virus; dengue virus; flavivirus; innate immunity; translation; viral RNA replication.

FIGURE 1

Schematic representation of flavivirus vRNA. (A) vRNA is composed of a 5′UTR, one single open reading frame and a 3′UTR. The position of the sequences encoding for the viral proteins within the polyprotein is indicated. The bottom part of the figure shows in details the secondary structures of 5′UTR, capsid-coding region and 3′UTR. The different regions engaged in local pseudoknots and long-range RNA–RNA interactions are indicated and described in detail in the text. (B) Predicted structure of vRNA in its circularized conformation. The coding sequence (except 5′ capsid coding region) is depicted with a dashed line.

FIGURE 2

A model of the different fates of vRNA. vRNA is replicated by NS5 within the vesicle packets (VP) with the assistance of other nonstructural proteins. Using vRNA, the positive strand (red), as a template, the synthesis of the negative strand (black) by NS5 is depicted. Subsequently, several new copies of vRNA are produced from the dsRNA replication intermediate (not shown). Translation presumably occurs outside of VPs since ribosomes can be visualized adjacent to these structures. vRNA is proposed to exit VPs through a pore to be directly encapsidated and enveloped into juxtaposed ER budding structures. Finally, vRNA is partially degraded by cellular XRN1 which generate sfRNA. sfRNA regulates several host responses including innate immunity at the levels of signal transduction and ISG translation.