Quantitative mapping of pseudouridines in bacteria RNA

RNA pseudouridylation is one of the most prevalent post-transcriptional modifications, occurring universally across all organisms. Although pseudouridines have been extensively studied in bacterial tRNAs and rRNAs, their presence and role in bacterial mRNA remain poorly characterized. Here, we used a bisulfite-based sequencing approach to provide a comprehensive and quantitative measurement of bacteria pseudouridines. As a proof of concept in E. coli, we identified 1,954 high-confidence sites in 1,331 transcripts, covering almost 30% of the transcriptome. Furthermore, pseudouridine mapping enabled the detection of differentially expressed genes associated with stress response that were unidentified using conventional RNA-seq approach. We also demonstrate that in addition to pseudouridine profiling, our approach can facilitate the discovery of previously unidentified transcripts. As an example, we identified a small RNA transcribed from the antisense strand of tRNA-Tyr which represses expression of distal genes. Finally, we mapped pseudouridines in oral microbiome samples of human subjects, demonstrating the broad applicability of our approach in complex microbiomes. Altogether, our work highlights the advantages of mapping bacterial pseudouridines and provides a tool to study posttranscription regulation in microbial communities.