An sRNA overexpression library reveals AbnZ as a negative regulator of an essential translocation module in Caulobacter crescentus

Small RNAs (sRNAs) play a crucial role in modulating target gene expression through short base-pairing interactions and serve as integral components of many stress response pathways and regulatory circuits in bacteria. Transcriptome analyses have facilitated the annotation of dozens of sRNA candidates in the ubiquitous environmental model bacterium Caulobacter crescentus, but their physiological functions have not been systematically investigated so far. To address this gap, we have established CauloSOEP, a multi-copy plasmid library of C. crescentus sRNAs, which can be studied in a chosen genetic background and under select conditions. Demonstrating the power of CauloSOEP, we identified sRNA AbnZ to impair cell viability and morphology. AbnZ is processed from the 3' end of the polycistronic abn mRNA encoding the tripartite envelope-spanning efflux pump AcrAB-NodT. A combinatorial approach revealed the essential membrane translocation module TamAB as a target of AbnZ, implying that growth inhibition by AbnZ is linked to repression of this system. Transcriptomic of Caulobacter NA100 ΔvanAB pBVMCS6-EV (KFS-96) & Caulobacter NA100 ΔvanAB pBVMCS6-AbnZ (KFS-1421) after 15´ of addition on 500 µM Vanillate to induce the sRNA. Cells were growing in PYE medium at 30°C until they reached OD660=0.4. 500 µM Vanillate was added to the cells and after 15´ samples were collected for RNAprep.