A short peptide derived from late embryogenesis abundant proteins enhances acid tolerance in Escherichia coli via modulation of two-component regulatory systems.

Late embryogenesis abundant (LEA) proteins are responsible for facilitating tolerance to various environmental stresses across diverse organisms. Group 3 LEA proteins are characterised by the presence of 11-mer amino acid motifs, which inspired the design of short peptides with similar protective functions. Here, we designed a LEA peptide variant (LEA-K) and evaluated its acid tolerance capacity in Escherichia coli BL21 (DE3) at pH4. Expression of LEA-K peptide improved the bacterial viability under acidic stress, suggesting its protective functions. To explore the molecular mechanism of such tolerance, we combined the RNA-sequencing (RNA-Seq) technique and molecular docking simulations. Transcriptome analysis identified 283 differentially expressed genes (DEGs), and revealed metabolic reprogramming and activation of stress-related pathways, including proton pumping, biofilm formation, and stress responsive systems. Functional enrichment analysis suggested a key role of two-component regulatory systems (TCSs) such as reactive chlorine species (RCS), sensor histidine kinase BtsS/transcriptional regulatory protein BtsR, and DNA-binding dual transcriptional regulator OmpR/sensor histidine kinase EnvZ. Protein-peptide docking simulations indicated potential interactions between LEA-K and these TCSs, suggesting a mechanistic basis of the observed transcriptional modulation. These findings propose previously unknown functional roles for LEA peptides, not only acting as molecular shields but also as signal-transducing modulators. This work expands our understanding of stress tolerance mechanisms and presents a new avenue for engineering stress-resilient bacterial systems.