RNA Structure Duplications and Flavivirus Host Adaptation

Abstract

Flaviviruses include a highly diverse group of arboviruses with a global distribution and a high human disease burden. Most flaviviruses cycle between insects and vertebrate hosts; thus, they are obligated to use different cellular machinery for their replication and mount different mechanisms to evade specific antiviral responses. In addition to coding for viral proteins, the viral genome contains signals in RNA structures that govern the amplification of viral components and participate in triggering or evading antiviral responses. In this review, we focused on new information about host-specific functions of RNA structures present in the 3' untranslated region (3' UTR) of flavivirus genomes. Models and conservation patterns of RNA elements of distinct flavivirus ecological groups are revised. An intriguing feature of the 3' UTR of insect-borne flavivirus genomes is the conservation of complex RNA structure duplications. Here, we discuss new hypotheses of how these RNA elements specialize for replication in vertebrate and invertebrate hosts, and present new ideas associating the significance of RNA structure duplication, small subgenomic flavivirus RNA formation, and host adaptation.

Keywords: RNA virus evolution; dengue virus; flaviviruses; host adaptation; sfRNAs; viral RNA structures.

Figure 1

Conserved Features and Mechanism of Flavivirus RNA Synthesis. a) Schematic representation of the distance tree of the four ecological groups of flaviviruses drawn using the neighbor joining method and jukes-cantor substitution model. b) Predicted RNA structure and sequence of SLA elements of different flaviviruses. c) General mechanism of viral RNA synthesis that involves the promoter element SLA at the 5’ end of the viral RNA, cyclization of the viral genome, and polymerase initiation at the 3’ end.

Figure 2

Plot of Sequence Conservation of the Four DENV Serotypes. The 3’ UTR is divided into three regions according to the sequence variability (regions I, II, and III). Below, is a secondary structure model of the 3’ UTR of DENV2 predicted by conservation, stability and chemical probing; deletions (red lines) or point mutations (circles) rescued from mosquito cell-adapted populations are indicated.

Figure 3

Representation of Local Analysis of RNA Structure Similarities Using the RNAforester Algorithm. Top, comparison of the duplicated structures SLI (SL5’, indicated in green) and SLII (SL3’ indicated in red) of members of the DENV group. A fan dendrogram indicating the distance between these structures is shown with the corresponding circle plot with the sequence and arcs denoting base pairings. Bottom, a similar comparison of SL5’ and SL3’ structures are shown for members of the JEV group. Bar indicates number of nucleotide substitution per site

Figure 4, Key Figure

New Functions of RNA Structures Present at the 3’ UTR of Mosquito-Borne Flaviviruses. Host adaptation selects different dengue virus populations and the link between RNA structure duplication, host adaptation, and production of subgenomic flavivirus RNAs (sfRNAs) is described. Red lines under each population illustrate the change in frequency of the same viral variant.

Figure 5

Models of Conserved RNA Structural Elements of Mosquito Borne Flavivirus 3’ UTRs. Schematic representation of RNA structures and conserved RNA motifs for each group (DENV, JEV and YFV) are shown. Below the models, an example of one member of each group (DENV2, WNV-LI, and YFV-17D) is shown using an Arc plot secondary structure representation, including the nucleotide sequence. The color code for each structural motif is maintained in all the representations. Pseudoknot interactions (PKs) are indicated underneath each Arc plot. Abbreviations: SL: stem-loop, DB: dumbbell, sHP: small hairpin, 3’ SL: 3’ stem-loop, UU-SL: U rich stem-loop, bt-SL: between stem-loop, YFVR: yellow fever virus repeat, ORF: open reading frame.

Figure 6

Models of Conserved RNA Structural Elements of Tick-Borne, No-Known Vector, and Insect-Specific Flaviviruses. Schematic representation of RNA structures and conserved RNA motifs for each group are shown. Below the models, an example of one member of each group is shown using an Arc plot secondary structure representation including the nucleotide sequence: Powassan virus (POWV), Modoc virus (MODV) and for insect specific flavivirus examples the cellular fusion agent virus (CFAV), Culex flavivirus CxFV), and Chaoyang virus (CHAOV) are included. The color code for each structural motif is maintained in all the representations. Pseudoknots interaction (PKs) are indicated underneath each Arc plot. Abbreviations: Y-SL: Y-shape stem-loop, AU-SL: AU containing stem-loop, GC-SL: GC containing stem-loop, DB: dumbbell, sHP: small hairpin, 3’ SL: 3’ stem-loop, AeSL: Aedes stem-loop, ORF: open reading frame.

Figure 7

Phylogenetic Relationships between Members of the Flavivirus Genus with Arch Representations of Conserved Structures of the Viral 3’ UTRs. Phylogenetic tree using coding regions of flaviviruses employing a neighbor-joining method is shown. 3’ UTR structures are represented in arc plots using the following color code: SL structures in orange, DB and ΨDB in pale blue, YFVR in brown, UU-SL in green, bt-SL in gray, YSL in violet, GC-SL in pink, AU-SL in pale green and sHP-3’ SL in blue. Mosquito-borne flavivirus taxonomic groups: DENV group, JEV group, YFV group, Aroa virus group (AROVG), Kokobera virus group (KOKVG), Ntaya virus group (NTAVG), and Spondweni virus group (SPOVG).