# Epitranscriptomic control of stress adaptations in Escherichia coli

## TL;DR

This study explores how RNA modifications in Escherichia coli help the bacteria adapt to stress, revealing a new layer of gene regulation.

## Contribution

The first comprehensive mapping of the bacterial epitranscriptome during early stress response using direct RNA sequencing and mass spectrometry.

## Key findings

- Widespread mRNA modifications were identified, including those in central metabolism transcripts.
- Stress-induced rRNA methylations (m4Cm and m5C) suggest a role in translation under stress.
- Stress-specific pre-tRNA modifications via Mnm and Q pathways are essential for bacterial survival.

## Abstract

The impacts of various stressors on bacterial systems have been studied at the phenotypic, transcriptional, and translational levels during the early stress response. However, the contributions of RNA modifications during stress adaptation remain largely unexplored. Here, we map the epitranscriptomic changes of Escherichia coli after exposure to oxidative and acid stress using direct RNA sequencing of mRNA, rRNA, pre-tRNA, and tRNA, combined with mass spectrometry, deletion mutant phenotyping, and single-nucleotide PCR. We identified widespread, dynamic mRNA modifications that include central metabolism transcripts and increased levels of rRNA methylations (m4Cm and m5C) under both stresses, with potential consequences for translation. In uncharged pre-tRNAs, stress-specific modifications via the Mnm and Q pathways accumulated at the wobble position; these modifications proved crucial for survival. Together, these findings reveal a multifaceted layer of post-transcriptional regulation, establishing the first comprehensive view of the bacterial epitranscriptome during the early stress response.

Graphical Abstract