Investigating alternative AUG usage in avian Influenza A virus segment 2

Influenza A viruses (IAV) have a segmented, negative sense RNA genome. PB1-F2 is an IAV accessory protein encoded by segment 2, in the +1 reading frame. IAVs from avian hosts generally encode full length PB1-F2s, which contrasts with human IAVs which frequently have C-terminal truncations. Many reported activities of PB1-F2, including innate immune antagonism, require motifs in its C-terminal domain. Full length PB1-F2 is translated from AUG 4 of segment two, but one or more of AUGs 7, 8 and 9 may also serve as independent initiation codons for the C-terminal domain. Products from the AUGs 7-9 are expressed during infection by a vaccine strain IAV, but their presence or absence had no effect on virus growth in vitro. We generated a panel of isogenic viruses, containing segment 2 from an avian H5N1 IAV, which differed in the presence or absence of the various AUG start codons in segment 2. No difference in growth kinetics in vitro or viral polymerase activity, measured using a mini-replicon assay, was observed for any of these mutants. However a significant difference in mean plaque size on MDCK cells was seen when individual changes were made to any of AUGs 7-9, suggesting a subtle effect on virus fitness possibly caused by loss of expression of PB1-F2 C-terminal fragments. In addition structural predictions suggest that the AUG mutations will affect secondary structure of full length PB1-F2. Our works suggests segment 2 protein expression from multiple AUGs could impact of the virus replication cycle.