Flagella are important for bacterial motility as well as for pathogenesis. Synthesis of these structures is energy intensive and, while extensive transcriptional regulation has been described, little is known about the posttranscriptional regulation. Small RNAs (sRNAs) are widespread posttranscriptional regulators, most base pairing with mRNAs to affect their stability and/or translation. Here we describe four UTR-derived sRNAs (UhpU, MotR, FliX and FlgO) whose expression is controlled by the flagella sigma factor {sigma}28 (fliA) in Escherichia coli. Interestingly, MotR and FliX have opposing effects on flagellin protein levels, flagella number and cell motility, with MotR accelerating flagella synthesis and FliX decelerating flagella synthesis. Unlike most sRNAs, MotR and FliX base pair within the coding sequences of target mRNAs. They also uniquely act on ribosomal protein mRNAs thus coordinating flagella synthesis with ribosome production. The study shows how sRNA-mediated regulation can overlay a complex network enabling nuanced control of flagella synthesis.
