Secondary structure model of the naked segment 7 influenza A virus genomic RNA

Abstract

The influenza A virus (IAV) genome comprises eight negative-sense viral (v)RNA segments. The seventh segment of the genome encodes two essential viral proteins and is specifically packaged alongside the other seven vRNAs. To gain insights into the possible roles of RNA structure both within and without virions, a secondary structure model of a naked (protein-free) segment 7 vRNA (vRNA7) has been determined using chemical mapping and thermodynamic energy minimization. The proposed structure model was validated using microarray mapping, RNase H cleavage and comparative sequence analysis. Additionally, the detailed structures of three vRNA7 fragment constructs - comprising independently folded subdomains - were determined. Much of the proposed vRNA7 structure is preserved between IAV strains, suggesting their importance in the influenza replication cycle. Possible structure rearrangements, which allow or preclude long-range RNA interactions, are also proposed.

Influenza virus segment 5 (+)RNA - secondary structure and new targets for antiviral strategies

“…a 3D structured loop) or alternative intermolecular interactions. Such a pattern of oligonucleotide binding is typical for structured RNA 11 , 12 , 31 , 33 . The accessibility to oligonucleotide binding gives information on regions that are prone to intermolecular interactions, as well as regions that are mostly single stranded or weakly paired.…”

“…Only several of these motifs have been examined experimentally, and very few have been studied in vivo 2 , 8 – 10 . Only for two entire viral genomic segments, 8 and 7, has secondary structure been determined 11 , 12 . The structural information derived for segment 8 was used for designing effecting antisense oligonucleotides (ASOs) that inhibited virus proliferation 13 .…”

A compensatory mutagenesis study of a conserved hairpin in the M gene segment of influenza A virus shows its role in virus replication

“…It should be noted that although nucleotide 986 is suggested to be paired in the M mRNA hairpin stem ( Fig. 1B ), it is likely to be located in the larger loop of the vRNA (negative sense) counterpart hairpin 5 , 26 due to the 986–975 AC mismatch that also makes the formation of the isolated neighboring base pair 985–976 unlikely. At nucleotide position 980 2 nucleotide changes were possible that resulted in silent mutations; consequently both U980A (LQ1) and U980C (LQ2) mutations were introduced.…”

“… 5 , 25 This hairpin was also detected by in vitro structure probing of protein-free M vRNA. 26 Several studies have investigated the region that spans this predicted M RNA structure. First, Hutchinson et al.…”

Frustration and Fidelity in Influenza Genome Assembly

“…Consistent with this idea, mutations in the conserved RNA terminal regions cause defects in genome packaging [12]- [16]. Genomic RNA strands are seen to physically bind in vitro and in vivo [17]- [19] via RNA base-pairing interactions [20]- [22] and interactions mediated by vRNP-associated proteins [23]- [25]. In addition to the equilibrium RNA-RNA binding measured in vitro, livecell imaging reveals that some inter-segment interactions are irreversible on the timescale of an infection [26].…”