A host enzyme pseudouridylates an RNA bacteriophage genome and accelerates virus production

Abstract

RNA modifications are prevalent and potent regulators of gene expression across all domains of life. However, whether they exist in bacteriophages and whether they impact phage-host interactions are largely unexplored. To address this, we leveraged the ssRNA bacteriophage MS2 and its E. coli host. Using quantitative nanopore direct RNA sequencing and pseudouridine profiling, we found that essentially all copies of MS2 genomic RNA are pseudouridylated at a single position within the maturation protein gene. Through analysis of the surrounding sequence context, analysis of predicted structure, and genetic assignment of the pseudouridine to its installing enzyme, we demonstrate that the bacterial host enzyme RluA is responsible for pseudouridylation of the phage genome. In the absence of host RluA, the latent and eclipse periods are extended, indicating that the enzyme is important to early stages of phage infectivity. We find that this pseudouridine is present at varying occupancies in additional ssRNA coliphages, also installed by host RluA, and that the conserved features of RluA substrates are present in diverse ssRNA phages with host species beyond E. coli. Altogether, our findings identify RNA modification as a feature of bacteriophage genomes and establish host RNA-modifying enzymes as a class of infection-modulating phage host factors.