FliA-Dependent Small RNAs Integrate Metabolism and Flagella Biosynthesis

Authors

• S Melamed
• J Mills
• A Zhang
• M Jarnik
• G Storz

Abstract

Flagella are important for motility as well as for pathogenicity. Flagella synthesis is extremely energy intensive and is under extensive transcriptional regulation. However, less is known about post-transcriptional regulation of flagella synthesis. Small RNAs (sRNAs) are widely utilized as posttranscriptional regulators; many base-pairing with mRNAs affecting their stability and/or translation. Yet, the only known target of the sRNAs in the flagella regulon is the flhDC mRNA encoding the transcription factor at the top of the regulatory network. Here we report on four Escherichia coli sRNAs whose expression is controlled by the flagella sigma factor, encoded by fliA. These sRNAs are mainly expressed in log phase and originate from the UTR regions of mRNAs, including three genes belonging to the flagella regulon, and add a post-transcriptional level to the already complex regulatory network controlling flagella synthesis. RIL-seq (RNA Interaction by Ligation and sequencing) identified multiple putative targets for these FliA-dependent sRNAs. Translational reporter assays together with in vitro structural probing validated several targets, showing two of the sRNAs modulate the synthesis of ribosomal proteins, which are required for the mass production of the flagella proteins. Another sRNA represses regulators of the flagellar regulon. Interestingly, electron microscopy shows that overexpression of each of the sRNAs leads to a unique phenotype in terms of flagella length and number. These phenotypes exemplify the diverse impact that sRNAs can have on complex regulatory networks. Taken together, these data demonstrate a novel level of regulation of the flagellar regulon that enables nuanced control of flagella synthesis.

Scientific Focus Area: Microbiology and Infectious Diseases

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