Regulatory Interplay between RNase III and Antisense RNAs in E. coli: the Case of AsflhD and FlhD, Component of the Master Regulator of Motility.

In order to respond to ever-changing environmental cues, bacteria display resilient regulatory mechanisms controlling gene expression. At the post-transcriptional level, this is achieved by a combination of RNA-binding proteins, such as ribonucleases (RNases), and regulatory RNAs, including antisense RNAs (asRNAs). Bound to their complementary mRNA, asRNAs are primary targets for the double-strand-specific endoribonuclease, RNase III. Taking advantage of our own and previously published transcriptomic data sets obtained in strains inactivated for RNase III, we selected several candidate asRNAs and confirmed the existence of RNase III-sensitive asRNAs for , , , and genes, all encoding global regulators of gene expression in Escherichia coli. Using FlhD, a component of the master regulator of motility (FlhDC), as our model, we demonstrate that the asRNA AsflhD, transcribed from the coding sequence of , is involved in the fine-tuning of expression and thus participates in the control of motility. The role of antisense RNAs (asRNAs) in the regulation of gene expression remains largely unexplored in bacteria. Here, we confirm that asRNAs can be part of layered regulatory networks, since some are found opposite to genes encoding global regulators. In particular, we show how an antisense RNA (AsflhD) to the gene, encoding the transcription factor serving as the primary regulator of bacterial swimming motility (FlhDC), controls expression, which in turn affects the expression of other genes of the motility cascade. The role of AsflhD highlights the importance of fine-tuning mechanisms mediated by asRNAs in the control of complex regulatory networks.