Bacteria differently regulate mRNA abundance to specifically respond to various stresses. Escherichia coli str. K-12 substr. MC4100

Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational level. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up- and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly-translated transcripts with high copy numbers, allowing reallocation of translation resources to undegraded and newly synthesised mRNAs Overall design: Comparing global transcriptional and translational control by mRNA-Seq and Ribosome Profiling (mRNA-Seq of ribosome protected fragments – RPF)