A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation

Temperature influences the structural and functional properties of cellular components, necessitating stress responses to restore homeostasis following temperature shift. The heat shock circuitry is well understood, but that controlling the E. coli cold-shock adaptation program is not. We found that during the growth arrest phase (acclimation) that follows shift to low temperature, protein synthesis increases and ORF-wide mRNA secondary structure decreases. We identified two components of an mRNA surveillance system that enable recovery of translation during acclimation: RNase R assures appropriate mRNA degradation and the Csps dynamically adjust mRNA secondary structure to globally modulate protein expression level. Csps also remodel their own mRNAs to tune their expression to cellular need. Thus, appropriate translation is dynamically adjusted with Csp control. The universality of Csps in bacteria suggests broad utilization of this control mechanism. Ribosome profiling, total RNA/mRNA-seq and DMS-seq data at 37°C and following cold shock in E. coli Please note that the samples with _1 and _2 (in the sample titles) represent biological replicates of the same experiments.