Functional RNA Elements in the Dengue Virus Genome

Leopoldo G Gebhard,Claudia V Filomatori,Andrea V Gamarnik

doi:10.3390/v3091739

Leopoldo G Gebhard, Claudia V Filomatori + Show 1 more

Open Access

https://doi.org/10.3390/v3091739

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Abstract

Dengue virus (DENV) genome amplification is a process that involves the viral RNA, cellular and viral proteins, and a complex architecture of cellular membranes. The viral RNA is not a passive template during this process; it plays an active role providing RNA signals that act as promoters, enhancers and/or silencers of the replication process. RNA elements that modulate RNA replication were found at the 5′ and 3′ UTRs and within the viral coding sequence. The promoter for DENV RNA synthesis is a large stem loop structure located at the 5′ end of the genome. This structure specifically interacts with the viral polymerase NS5 and promotes RNA synthesis at the 3′ end of a circularized genome. The circular conformation of the viral genome is mediated by long range RNA-RNA interactions that span thousands of nucleotides. Recent studies have provided new information about the requirement of alternative, mutually exclusive, structures in the viral RNA, highlighting the idea that the viral genome is flexible and exists in different conformations. In this article, we describe elements in the promoter SLA and other RNA signals involved in NS5 polymerase binding and activity, and provide new ideas of how dynamic secondary and tertiary structures of the viral RNA participate in the viral life cycle.

Highlights

DENV Life CycleDengue virus (DENV) is a member of the Flavivirus genus of the Flaviviridae family [1]
The process begins with the synthesis of a negative strand RNA, which serves as template for the amplification of additional positive strand genomic RNA
This study indicated that conserved secondary structures were present at the 5' end of West Nile virus (WNV), Saint Louis encephalitis virus (SLEV), DENV, yellow fever virus (YFV), and Murray Valley encephalitis virus (MVEV) [12]

Summary

Introduction

Dengue virus (DENV) is a member of the Flavivirus genus of the Flaviviridae family [1]. Flaviviruses are enveloped viruses with a single stranded, ~11 kb, positive-sense RNA genome. Translation of the single ORF at the rough ER produces a large polyprotein that is cleaved co- and posttranslationally into the mature proteins. After translation of the RNA, virus-induced hypertrophy of intracellular membranes occurs, originating structures known as convoluted membranes and vesicle packets [3,4,5]. Flavivirus RNA synthesis occurs in close association with cellular membranes inside the vesicle packets in so-called viral replication complexes. The process begins with the synthesis of a negative strand RNA, which serves as template for the amplification of additional positive strand genomic RNA. The RNA-C complex buds into the ER lumen acquiring the lipid bilayer, and the viral E and prM proteins. Furin-mediated proteolysis of prM in the trans-Golgi network [6] triggers rearrangement, homodimerization of E, and formation of new viral particles [7]

RNA Structures in the DENV Genome

Functional Significance of DENV Genome Cyclization

Elements of the SLA Promoter for NS5 Binding and Polymerase Activity

Elements Downstream of the SLA that Modulate RNA Synthesis

Dynamic Conformations of the DENV Genome Are Necessary for RNA Synthesis

Future Prospects