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 machineries 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.

Interactions between the Dengue Virus Polymerase NS5 and Stem-Loop A

“…Flavivirus polymerase specifically recognizes the viral 5= UTR during viral RNA replication (24,25). In particular, SLA within the 5= UTR is predicted to form a "Y"-shaped secondary structure and serves as a promoter for NS5 polymerase binding and activity (25,27). Specific binding between NS5 and SLA was observed when SLA (70 nucleotides [nt]) had an additional ssRNA region at the 3= end ( Fig.…”

“…Specific binding between NS5 and SLA was observed when SLA (70 nucleotides [nt]) had an additional ssRNA region at the 3= end ( Fig. 1) (25,27). We thus constructed SLA with an additional 10 nt, containing the first 80 nt of the dengue virus genome, referred to here as SLA 80 , to study the interaction between SLA and NS5.…”

“…In particular, the 5= UTR contains two stem-loops, stem-loop A (SLA) and stem-loop B (SLB), and SLA has been shown to function as a promoter for RNA synthesis during the replication process (24)(25)(26). The importance of SLA in viral RNA replication has been demonstrated for several flaviviruses (24,27,28). Despite the importance of SLA in initiating dengue virus RNA replication, interactions between NS5 and SLA have not been quantitatively analyzed, and thus, fundamental aspects of the NS5-SLA interaction, such as stoichiometry and energetics of intrinsic affinities, are unknown.…”

Noncoding Subgenomic Flavivirus RNA Is Processed by the Mosquito RNA Interference Machinery and Determines West Nile Virus Transmission by Culex pipiens Mosquitoes

“…sfRNA production is conserved for all MBFs and TBFs, and although recent RNA structure analysis of ISF 3= UTRs failed to identify XRN1-resistant structures (33,34), it was previously reported that ISFs and NKVFs have conserved SL structures with putative pseudoknot structures in their 3= UTRs (35). Indeed, sfRNA production has been experimentally shown for several NKVFs and the ISF cell-fusing agent virus (36).…”

Biochemistry and Molecular Biology of Flaviviruses

“…485,486 The Gamarnik laboratory demonstrated that the evolutionary pressure on xrRNA2 sequences from DENV2 is different in mammalian and mosquito cells. 487 In mosquitos mutations that disrupt Xrn1 resistance appear, resulting in shorter sfRNA species, sfRNA2, sfRNA3, and sfRNA4 (see Figure 1), while in human cells sfRNA1 is the predominant product. 113 Mosquito-adapted DENV2 that produced shorter sfRNAs had a fitness disadvantage and triggered an increased immune response (IFN β and ISG15 gene expression) in human cells, but the same virus did not have an altered replication rate when grown in mosquito cells.…”