The cut site specificity of the influenza A virus endoribonuclease PA-X allows it to discriminate between host and viral mRNAs

Abstract

Widespread shutoff of host gene expression through RNA degradation is an advantageous way for many viruses to block antiviral responses. However, viruses need to maintain expression of their own genes and host genes necessary for replication despite the RNA degradation. The influenza A virus host shutoff endoribonuclease PA-X solves this problem by discriminating between RNAs and sparing viral mRNAs and some host RNAs. To understand how PA-X distinguishes between RNAs, we identified and characterized PA-X cut sites transcriptome-wide. This analysis shows that PA-Xs from multiple influenza strains cleave RNAs at GCUG tetramers in hairpin loop structures. Importantly, GCUG tetramers are enriched in the human but not the influenza transcriptome. This finding suggests that PA-X evolved these cleavage characteristics to target host but not viral mRNAs. Our study reveals a new layer of PA-X specificity, and shows how viral endoribonuclease cleavage specificity plays a functional role to selectively target the host.