RNA structure interactions and ribonucleoprotein processes of the influenza A virus

Dawson, Wayne K; Lazniewski, Michal; Plewczynski, Dariusz

The results from Kobayashi et al. only look at Segment 7; they do not specify where these hairpins might bind to other segments of the vRNP. However, the kissing loop reported in Gavazzi et al. [84] can also be examined in this way. Figure 5 shows a scan of Segments 2 and 8 for the same corresponding vRNA sequence reported in [84] , strain A/finch/England/2051/1991(H5N2). The same default settings are used as above for vswindow/Genepoem. Likewise, in Figure 5 , the two connected semi-opaque gray/green boxes is used to indicate the corresponding sequence ranges reported in Gavazzi et al. [84] , and the dashed lines indicate the connection between Segment 2 and Segment 8. Though both Segment 2 and Segment 8 are clearly visible in the spectrum-indicating that the structures are relatively stablethe intensity of the gray/blue in these regions is less than some other cases in the same spectrum. This lower intensity gray/blue indicates that there is a greater degree of variation in the RNA secondary structure in these locations. In line with the observation that the linking together of vRNPs is the result of kissing hairpins, this may suggest that there are many such contacts regularly dispersed along the vRNA segments that act like a bar code that defines how the pieces should be fit together with one another and identify the vRNPs specific to a particular strain. Though this may diminish some of the long-held fears of facile reassortment of the common flu with such strains as H5N1, it also could explain how individual strains evolve and compete with one another too.