Viruses are obligate intracellular parasites that, throughout evolution, have adapted numerous strategies to control the translation machinery, including the modulation of post-transcriptional modifications (PTMs) on
transfer RNA (
tRNA). PTMs are critical translation regulators used to further host immune responses as well as the expression of
viral proteins. Yet, we lack critical insight into the temporal dynamics of
infection-induced changes to the
tRNA modification landscape (i.e., 'modificome'). In this study, we provide the first comprehensive quantitative characterization of the
tRNA modificome in the marine bacterium Shewanella glacialimarina during Shewanella phage 1/4
infection. Specifically, we show that PTMs can be grouped into distinct categories based on modification level changes at various
infection stages. Furthermore, we observe a preference for the UAC
codon in viral transcripts expressed at the late stage of
infection, which coincides with an increase in
queuosine modification.
Queuosine appears exclusively on tRNAs with GUN
anticodons, suggesting a correlation between phage codon usage and PTM modification. Importantly, this work provides the basis for further studies into
RNA-based regulatory mechanisms employed by bacteriophages to control the prokaryotic translation machinery.