# 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

## TL;DR

This study explores how bacteria like E. coli and P. aeruginosa from patient infections use RNA editing to change protein functions, revealing new insights into this process in clinical settings.

## Contribution

The first comprehensive analysis of A-to-I RNA editing in pathogenic E. coli and P. aeruginosa isolates from hospitalized patients.

## Key findings

- E. coli exhibits higher RNA editing levels and more editing sites than P. aeruginosa.
- Most editing sites are within a conserved 7-base motif and in RNA stem-loop structures.
- Editing often results in nonsynonymous amino acid changes, including tyrosine-to-cysteine substitutions.

## Abstract

Adenosine-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.

We 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.

We 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.

Adenosine-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.

Here, we describe the occurrence, regulatory features, and predicted effect of RNA-specific sequence changes resulting from A-to-I RNA editing in E. coli and P. aeruginosa isolates obtained from hospitalized patients.