Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs

Primary data from paper "Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs".

Abstract:  Many viruses block host gene expression to take over the infected cell. This process, termed host shutoff, is thought to promote viral replication by preventing antiviral responses and redirecting cellular resources to viral processes. Several viruses from divergent families accomplish host shutoff through RNA degradation by endoribonucleases (endoRNases). However, viruses also need a way to maintain expression of their own genes. Influenza A virus host shutoff endoribonuclease PA-X solves this problem by sparing viral mRNAs and some host RNAs necessary for  replication. To understand how PA-X distinguishes between RNAs, we characterized PA-X cut sites transcriptome-wide using 5’ rapid amplification of cDNA ends (5’ RACE) coupled to high-throughput sequencing. This analysis, along with experimental validation using 5’ RACE on mutated reporters, shows that PA-Xs from multiple influenza strains preferentially cleave RNAs at GCUG tetramers in hairpin loops. Importantly, GCUG tetramers are enriched in the human but not the influenza transcriptome. Moreover, optimal PA-X cut sites inserted in the influenza A virus genome are quickly selected against during viral replication in cells. This finding suggests that PA-X evolved these cleavage characteristics to preferentially target host over viral mRNAs, in a manner reminiscent of cellular self vs. non-self discrimination.