Effects of temperature on specificity and efficiency of a bacterial regulatory RNA

Bacterial small RNAs (sRNAs) are post-transcriptional regulators of stress response, virulence and more. The activity of sRNAs must be maintained across diverse environmental conditions, including the range of temperatures that defines the thermal niche of the species. Here we characterize the effects of temperature on the specificity and efficiency of sRNA regulation in E. coli. By measuring the activity of a large-scale library of sRNA variants at different temperatures, we found that many mutations have a significant but temperature-independent effect. We identified temperature-sensitive sequence elements using measurements that break from this dominant trend. Features associated with the specificity of sRNA regulation are more sensitive to mutations at high temperatures, and we confirm that specificity is more stringent at these temperatures. In contrast, many mutations in the region responsible for interactions with other targets have a stronger negative impact at low temperatures. Together, our results suggest that sRNAs may be structured such that variation in temperature may enhance their evolutionary plasticity. Sort-seq assays across a range of bacterial growth temperatures from 21 C to 37 C