Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA

Research into post‐transcriptional control of mRNAs by small noncoding RNAs (sRNAs) in the model bacteria Escherichia coli and Salmonella enterica 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 Salmonella 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 trans the mRNA of histone‐like protein HU‐α. RaiZ forms an RNA duplex with the ribosome‐binding site of hupA 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. Synopsis The enterobacterial sRNA RaiZ functions independent of the Hfq RNA chaperone via the recently identified general RNA‐binding protein ProQ. ProQ acts in a dual manner, stabilizing the sRNA and facilitating translational repression of the nucleid protein HU‐α. RaiZ is a small RNA produced by RNase E‐mediated cleavage of the raiA mRNA. RaiZ strongly binds RNA chaperone ProQ, leading to RaiZ stabilization. RaiZ represses translation of the hupA mRNA by base pairing with its ribosome‐binding site. ProQ and RaiZ jointly prevent initiating ribosomes from loading on hupA mRNA. Graphical Abstract The global RNA‐binding protein ProQ stabilizes bacterial small RNA RaiZ and facilitates translational repression of its target mRNA, thus exemplifying an Hfq‐independent RNA regulon.