Small RNAs (sRNAs) contribute significantly to post-transcriptional regulation in bacteria and influence stability and translation of target mRNAs through direct base-pairing interactions. The oligotrophic Alphaproteobacterium Caulobacter crescentus encodes more than one hundred sRNAs however the cellular role of the majority of these non-coding regulators is currently unknown.
We have used genetic and biochemical approaches to characterize two Caulobacter sRNAs, ChvX and ChvY, which are encoded in tandem. Both sRNAs share significant similarity in sequence and structure, and are transcriptionally regulated by the conserved two-component system (TCS) ChvIG. Global transcriptome analyses upon ChvX and ChvY pulse expression revealed a largely overlapping pool of target candidates for both sRNAs, but also a small set of mRNAs only responding to either ChvX or ChvY. Employing a GFP-reporter system we have verified direct post-transcriptional regulation of targets, and confirmed predicted base-pairing interactions through compensatory exchanges in both RNA interaction partners.