Figure 3.

Schematic of the ORFs and encoded protein domain structures of the 5′-end of segment 2, 3, 5, and 6 mRNAs. Boxes represent ORFs in each of the three reading frames (Fr) or the major polypeptide species and their functional domains (top bars). AUG codons are represented by vertical lines, colored according to the predicted strength of their Kozak translation initiation context (green, strong; amber, intermediate; red, weak). Black arrows indicate AUGs known to be used for translation initiation for the indicated proteins. Gray arrows indicate AUG codons proposed to fire on the basis of ribosomal profiling data. (A) Represents the first 900 nucleotides of the PR8 sequence. Thin brackets indicate the approximate location of two sequence elements proposed to negatively regulate (blunt arrow) PB1-F2 expression. (Panel adapted from data in Figure 1A of Wise et al. 2009.) (B) Represents the first 900 nucleotides of PR8 sequence; note that in this (and most IAV strains), PA-N155 and -N182 are initiated from the 13th and 15th AUG codons in the segment, respectively. The stepped arrow indicates the +1 ribosomal frameshift event that accesses the X-ORF to produce PA-X. The gray line in the X-ORF indicates a common length polymorphism present in the H1N1pdm09 virus lineage. (C) Represents the first 150 nucleotides of A/England/195/2009 (H1N1) sequence, as well as downstream sequences around 450 nucleotides. (D) Represents the first 150 nucleotides of the WSN sequence.