Characterization of PA-N terminal domain of Influenza A polymerase reveals sequence specific RNA cleavage

Influenza virus uses a unique cap-snatching mech-anism characterized by hijacking and cleavage of host capped pre-mRNAs, resulting in short capped RNAs, which are used as primers for viral mRNA synthesis. The PA subunit of influenza polymerase carries the endonuclease activity that catalyzes the host mRNA cleavage reaction. Here, we show that PA is a sequence selective endonuclease with distinct preference to cleave at the 30 end of a guanine (G) base in RNA. The G specificity is ex-hibited by the native influenza polymerase complex associated with viral ribonucleoprotein particles and is conferred by an intrinsic G specificity of the isolated PA endonuclease domain PA-Nter. In addition, RNA cleavage site choice by the full poly-merase is also guided by cap binding to the PB2 subunit, from which RNA cleavage preferentially occurs at the 12th nt downstream of the cap. However, if a G residue is present in the region of 10–13 nucleotides from the cap, cleavage preferen-tially occurs at G. This is the first biochemical evidence of influenza polymerase PA showing intrin-sic sequence selective endonuclease activity