Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses
Fig 7
Examples of predicted structures near the PA/PA-X frameshift.
Predictions are shown using RNAalifold [18] on sections of the alignments for the labelled subtypes, with the fourth position in the slippery site UCC_UUU_CGU marked with black arrows and numbered “+1”. Folding was performed on subsequences beginning before and ending after this position as indicated in the labels; these subsequences correspond to regions deemed constrained by our algorithm. Where a long region was folded, only the portion of the fold containing the slippery site and stem-loop is displayed (where this results in discontinuous display of a portion of nucleic acid, a nucleotide is labelled to give its position in relation to the slippery site). Possible GAAA (in some cases with an A substituted by G) motifs that can base pair with the UUUC of the slippery site are marked in orange. A number of possible base pairings leading to stem-loop motifs are predicted. We postulate that an ensemble of such stem-loops is in fact seen, with the composition of the ensemble capable of modifying the relative PA/PA-X abundances (see main text): the differing predicted secondary structures would therefore arise because small differences in the input data result in the algorithm used reaching different, but numerically very close, modified free energy minima. Predicted structures for analysed but not shown subtypes have similar topology to one of the structures displayed (S3–S8 Figs).