Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure‐specific manner

Abstract

Protein kinase PKR is a key component of innate immunity. It is activated by long stretches of dsRNA and functions to inhibit translation initiation. Many cellular and viral transcripts contain nucleoside modifications which could affect PKR activation. For example, a 5′‐triphosphate confers the ability of relatively unstructured transcripts to activate PKR. Herein, PKR activation by ssRNA and dsRNA containing internal nucleobase, sugar, and phosphodiester modifications is analyzed. We find that for 5′‐triphosphate‐containing ssRNA, most base and sugar modifications abrogate activation, although 2′‐fluoro‐modified ssRNA does not, indicative of a critical role for hydrogen bonding at the ribose sugar. In the case of dsRNA, a more limited set of nucleoside modifications affect PKR activation. Surprisingly, GU wobble pairs also largely abrogate dsRNA‐mediated activation when present at modest levels. Overall, the findings indicate that nucleoside modifications and wobble pairing may serve to discriminate self‐RNA and pathogenic RNA in innate immunity.