The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae
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ABSTRACT:
PROVIDER: PRJEB93809 | ENA |
REPOSITORIES: ENA
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Project description:RNA modifications have a substantial impact on tRNA function. While modifications in the anticodon loop play an important role in translational fidelity, modifications in the tRNA core influence tRNA structural stability. In bacteria, tRNA modifications play important roles in the stress response and expression of virulence factors. While tRNA modifications are well characterized in a few model organisms, our knowledge of tRNA modifications in human pathogens, such as Pseudomonas aeruginosa is lacking. Here we leveraged two orthogonal approaches to build a reference landscape of tRNA modifications in E. coli, which we used to identify tRNA modifications in P. aeruginosa. We determined conservation for many modifications between the two organisms. We also identified potential sites of tRNA modification in P. aeruginosa tRNA that are not present in E. coli. One of these sites is found at the same positions as acacp3U, a modification previously identified in Vibrio cholerae. Identifying which modifications are present on different tRNAs will uncover the pathways impacted by the different tRNA modifying enzymes, some of which may play roles in determining virulence and pathogenicity.
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Project description:tRNAs are heavily decorated with post-transcriptional modifications (tRNA modifications). Profile of tRNA modifications in non-model organisms are largely uncharacterized. Here using high-throughput sequencing, sites and frequency of tRNA modifications are predicted in Vibrio cholerae and Escherichia coli. During cDNA synthesis, some modifications cause misincorporation of a wrong base or termination of reverse transcription (RT). Using these RT-derived signatures we aim to explore organism-specific modifications and to track changes in modification frequency among different cellular conditions.
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Project description:This study is an analysis of changes in gene expression during stringent response in Vibrio cholerae. V. cholerae cells in mid-log were treated with serine hydroxamate and gene expression was compared to untreated cells. Keywords: Stress response, stringent response
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Project description:RNA modifications are fundamental to regulating essential cellular processes, including RNA folding, stability, gene expression, and the accuracy and efficiency of decoding. These modifications are added post-transcriptionally by specialized enzymes, yet their broader roles beyond RNA modification remain poorly understood. In this study, we uncovered a novel function for Vibrio cholerae tRNA dihydrouridine synthase B (VcDusB) in bacterial adaptation to oxidative stress. While VcDusB is traditionally recognized for catalyzing the reduction of uridine to dihydrouridine in tRNA, our findings revealed that its deletion severely compromises V. cholerae survival under hydrogen peroxide-induced oxidative stress. Unexpectedly, VcDusB not only modulated codon decoding efficiency at its target tRNAs, but also influenced global translation, including codons unrelated to its canonical substrates—a phenomenon particularly evident under oxidative stress conditions. Proteomic analysis of the ∆dusB strain exposed a substantial reduction in protein synthesis, highlighting a widespread translational defect in response to stress. Strikingly, point mutations in DusB demonstrated that its protective role during stress was independent of its tRNA modification activity. Instead, its ability to bind tRNA and its NADPH oxidase activity proved vital for survival. These findings reveal a previously unrecognized, non-canonical function of DusB in oxidative stress defense, expanding our understanding of RNA-modifying enzymes. More broadly, this work paves the way for investigating the multifaceted roles of these enzymes in cellular metabolism and stress responses, far beyond their established functions in RNA modification
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