Sigma 28-dependent small RNAs regulate timing of flagella biosynthesis

Synthesis of flagella is very energy intensive and, while extensive transcriptional regulation has been described, little is known about the post-transcriptional 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 in Escherichia coli. UhpU, MotR and FliX have distinct impacts on flagellin levels, flagella number and swimming, with MotR accelerating flagella synthesis and FliX decelerating flagella synthesis. Interestingly, MotR and FliX are noncanonical in that they base pair within the coding sequences of target genes. We characterize their respective positive and negative effects on genes encoding ribosomal proteins. Total RNA sequencing of E. coli strains carrying a control vector or overexpressing MotR* or FliX-S