RIL-seq analysis identifies the sRNA CrfA as an RNA sponge rewiring carbon starvation in Caulobacter

Caulobacter crescentus is an environmental bacterium living in nutrient-poor habitats. Adaptation of Caulobacter to changing physiological conditions has been extensively studied at the transcriptional level, but little is known about post-transcriptional control. In bacteria, small regulatory RNAs (sRNAs) contribute significantly to this layer of regulation by base-pairing mRNA targets, often with the help of RNA-binding proteins (RBPs), of which Hfq is the only one known to interact with sRNAs in Caulobacter.

To study the global Hfq-dependent RNA interactome in this species, we performed RIL-seq (RNA interaction by ligation and sequencing). Among the more than 1,000 new RNA-RNA interactions recovered in our analysis, we detected an abundant RNA pair involving the two sRNAs CrfA and R0014. CrfA has been previously identified in the Caulobacter response to carbon starvation, however, we now show that instead of acting directly on mRNA targets, CrfA functions as an RNA sponge, sequestering and inactivating the sRNA R0014. In turn, R0014 is a classical sRNA that base-pairs and represses its various target mRNAs encoding outer membrane receptors and components of the central metabolism.

Our study uncovers CrfA as an important non-coding regulator involved in rewiring the transcriptome of Caulobacter under low nutrient conditions, and to prime the bacterium for future outgrowth.