Differential Expression Of Small Rnas Under Chemical Stress And Fed-batch Fermentation In Escherichia Coli

Introduction: Bacterial small RNAs (sRNAs) are often expressed in response to changing environmental conditions and function to modulate gene expression. Although chemical stress is routinely encountered in microbial processing applications, the cellular response and the involvement of sRNAs in this process is poorly understood. We have used RNA sequencing to map the Escherichia coli sRNome during chemical stress and high cell density fermentations with the aim of identifying sRNAs involved in the stress response and those with potential roles in stress tolerance.Methods: RNA sequencing libraries were prepared from RNA isolated from E. coli MG1655 cells subjected to chemical stress with twelve compounds. The strain was also grown under high cell density fermentation conditions, where cells were harvested in four growth phases.Results: We have discovered over 250 novel intergenic transcripts, adding to the roughly 200 previously reported sRNAs in E. coli. There are 84 and 139 differentially expressed sRNAs under fermentation and chemical stress conditions, respectively. In the latter case, approximately 30 exhibit significant expression changes in multiple conditions, suggesting their involvement in a more general chemical stress response.Conclusions: This study has revealed a wealth of hitherto undescribed sRNAs and an atlas of expression under 17 growth conditions. A significant fraction of the sRNAs exhibit specific expression patterns during fermentation, and a group of them are differentially expressed in the presence of multiple chemicals, suggesting they may play regulatory roles during these stress conditions. These are candidates for improving stress tolerance and our understanding of the regulatory network during fermentation.