Molecular mechanism of mRNA repression in <i>trans</i> by a ProQ‐dependent small RNA

Abstract

Research into post-transcriptional control of mRNAs by small noncoding RNAs (sRNAs) in the model bacteria <i>Escherichia coli</i> and <i>Salmonella enterica</i> has mainly focused on sRNAs that associate with the RNA chaperone Hfq. However, the recent discovery of the protein ProQ as a common binding partner that stabilizes a distinct large class of structured sRNAs suggests that additional RNA regulons exist in these organisms. The cellular functions and molecular mechanisms of these new ProQ-dependent sRNAs are largely unknown. Here, we report in <i>Salmonella</i> Typhimurium the mode-of-action of RaiZ, a ProQ-dependent sRNA that is made from the 3' end of the mRNA encoding ribosome-inactivating protein RaiA. We show that RaiZ is a base-pairing sRNA that represses in <i>trans</i> the mRNA of histone-like protein HU-α. RaiZ forms an RNA duplex with the ribosome-binding site of <i>hupA</i> mRNA, facilitated by ProQ, to prevent 30S ribosome loading and protein synthesis of HU-α. Similarities and differences between ProQ- and Hfq-mediated regulation will be discussed.