Bacterial sRNAs are 50-400 nucleotide-long RNA molecules, most of which exert their regulation by base-pairing with their target mRNAs. In many bacteria, including Escherichia coli, the interaction between an sRNA and its targets is mediated by the Hfq protein, resembling the situation in eukaryotic cells where the interaction of a microRNA and its targets involves Argonaut. While it is widely accepted that miRNAs guide Argonaute proteins to their specific targets through sequence complementarity, the dynamics of sRNA-Hfq-target interaction, to the best of our knowledge, has not been yet fully determined. As a first step towards this question, we study the relationship between the levels of Hfq-bound sRNA and its target mRNAs. More specifically, we aim to measure the change in Hfq-bound target mRNA levels following a change in the expression level of their sRNA regulator. To this end we applied RNA-seq to measure the levels of total RNA and RNA co-IPed with Hfq from three E. coli strains (MG1655 Hfq-FLAG, MG1655 hfq::kan and MG1655 Hfq-FLAG rnc14::Tn10) with and without overexpression of the sRNA MicA. Our results indicate that most MicA target mRNAs, as well as MicA itself, were enriched in Hfq when MicA was overexpressed. In contrast, most target mRNAs of other sRNAs were depleted. In conclusion, our initial results indicate that there is a relationship between sRNA and target mRNA levels on Hfq, offering a strategy to identify putative novel targets.
