Switching off small RNA regulation with trap-mRNA

Small non-coding regulatory RNAs in bacteria have been shown predominantly to be tightly regulated at the level of transcription initiation, and sRNAs that function by an antisense mechanism on trans-encoded target mRNAs have been shown or predicted to act stoichiometrically. Here we show that MicM, which silences the expression of an outer membrane protein, YbfM under most growth conditions, does not become destabilized by target mRNA overexpression, indicating that the small RNA regulator acts catalytically. Furthermore, our regulatory studies suggested that control of micM expression is unlikely to operate at the level of transcription initiation. By employing a highly sensitive genetic screen we uncovered a novel RNA-based regulatory principle in which induction of a trap-mRNA leads to selective degradation of a small regulatory RNA molecule, thereby abolishing the sRNA-based silencing of its cognate target mRNA. In the present case, antisense regulation by chb mRNA of the antisense regulator MicM by an extended complementary sequence element, results in induction of ybfM mRNA translation. This type of regulation is reminiscent of the regulation of microRNA activity through target mimicry that occurs in plants.