RNA-Seq and Ribo-Seq analyses of the study "tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa"

The success of bacterial pathogens depends on the coordinated expression of virulence determinants. Regulatory circuits that drive pathogenesis are complex, multilayered, and incompletely understood. Here, we reveal that alterations in tRNA modifications define pathogenic phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. We demonstrate that the enzymatic activity of GidA leads to the introduction of a carboxymethylaminomethyl modification in selected tRNAs. Modifications at the wobble uridine base (cmnm5U34) of the anticodon drives translation of transcripts containing rare codons. Specifically, in P. aeruginosa the presence of GidA-dependent tRNA modifications modulates expression of genes encoding virulence regulators, leading to a cellular proteomic shift toward pathogenic and well-adapted physiological states. Our approach of profiling the consequences of chemical tRNA modifications is general in concept. It provides a paradigm of how environmentally driven tRNA modifications govern gene expression programs and regulate phenotypic outcomes responsible for bacterial adaption to challenging habitats prevailing in the host niche. Overall design: Pseudomonas aeruginosa UCBPP-PA14 mutant strains were planktonically cultured in LB to an OD600 of 0.4 (ribo seq experiment) or 2 (RNA seq experiment).domonas aeruginosa UCBPP-PA14 wild type and mutants strains cultivated in LB