Quantitative RNA pseudouridine landscape reveals dynamic modification patterns and evolutionary conservation across bacterial species

Here, we present the first comprehensive transcriptome-wide mapping of Ψ modifications across five diverse bacterial species (Klebsiella pneumoniae, Escherichia coli, Bacillus cereus, Pseudomonas aeruginosa, Pseudomonas syringae) using bisulfte-induced deletion sequencing at single-base resolution. Ψ modifications exhibit enriched distribution in coding sequences and notable conservation across orthologous genes involved in central metabolism.

Comparative analysis revealed evolutionarily conserved modification patterns in operons, such as the atp operon, and growth phase-dependent dynamics, particularly elevated modification levels in transfer RNA T-arms and transfer-messenger RNAs under stress conditions. We uncovered that Ψ modifications modulate mRNA translation in Pseudomonas syringae under nutrition-limited condition and enhance interactions with the RNA chaperone Hfq in Pseudomonas aeruginosa under stationary growth phase.