Abstract
In bacteria, regulatory networks controlling the adaptation of gene expression in response to stress are frequently complemented by base-pairing small regulatory RNAs (sRNAs) that act at the post-transcriptional level. While many regulatory circuits governing stress resilience have been studied in the model bacterium Caulobacter crescentus, only a small fraction of its diverse sRNA repertoire has been characterized. In this study, we globally identify interacting RNA-RNA pairs associated with the major RNA-binding protein Hfq in C. crescentus. In addition to numerous connections between sRNAs and mRNAs, we also recover RNA-RNA pairs consisting of two non-coding transcripts. Our results indicate that the sRNA CrfA acts as a sponge to inactivate a family of four conserved sRNAs, SisA-D. When induced by carbon starvation, CrfA redirects gene expression towards the utilization of distinct energy sources, and loss of the RNA sponge is linked to a severe growth defect in environments with fluctuating nutrient availability.