The Landscape and Regulatory Determinants of A-to-I RNA Editing in Escherichia coli and Pseudomonas aeruginosa Isolated From Patients With Urinary Tract and Ear Infections.

backgroundAdenosine-to-inosine (A-to-I) mRNA editing can alter protein sequence and function, enabling bacteria to express two RNA and protein versions encoded by the same gene. However, its prevalence and significance in clinical bacterial settings remain unclear.

methodsWe collected ten Escherichia coli and seven Pseudomonas aeruginosa isolates from hospitalized patients with urinary tract infections (UTI) or ear infections. Whole-genome and transcriptome sequencing were performed for each isolate, followed by Sanger sequencing for selected sites.

resultsWe present the first comprehensive analysis of A-to-I RNA editing in pathogenic bacteria isolated from hospitalized patients. We identified dozens of A-to-I RNA editing sites, including novel sites not previously reported in nonpathogenic E. coli and P. aeruginosa strains. We found that E. coli exhibits higher editing levels and a greater number of editing sites than P. aeruginosa. Most editing sites are embedded within a conserved 7-base motif and are frequently located in predicted stem-loop RNA secondary structures, highlighting the importance of both sequence and structure for editing site recognition in both the examined species. Most editing events occur in mRNA and often result in nonsynonymous amino acid changes, with a notable prevalence of tyrosine-to-cysteine substitutions. Finally, we observed that editing patterns are similar between antibiotic-resistant and sensitive isolates, suggesting a more general role in the biology of the examined species.

conclusionsAdenosine-to-inosine RNA editing is a feature of pathogenic bacteria isolated from clinical samples. Our findings expand current knowledge of bacterial RNA editing in clinical contexts and provide a framework for future functional investigations.