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

ABSTRACT: Pseudouridine (Ψ) modifications play crucial roles in RNA regulation, yet their distribution and functional significance in bacteria remain largely unexplored compared to eukaryotic systems. 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. We found local RNA architecture significantly influences modification levels, with highly modified sites sharing distinct structural features reminiscent of different type of RNA. To facilitate broader studies, we developed an integrated deep learning framework combining convolutional neural networks with transformer architecture to effectively capture both sequence patterns and RNA secondary structural features, enabling accurate prediction of Ψ modification sites across bacterial transcriptomes. Overall, our study provides fundamental insights into bacterial RNA Ψ modification landscapes and establishes a foundation for future mechanistic studies.

ORGANISM(S): Escherichia coli K-12 Pseudomonas aeruginosa PAO1 Bacillus cereus ATCC 14579 Klebsiella pneumoniae Pseudomonas savastanoi pv. phaseolicola 1448A

PROVIDER: GSE292335 | GEO | 2026/05/11

REPOSITORIES: GEO