Abstract
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.
Highlights
Many if not all organisms use small base-pairing RNAs to modulate mRNA expression at the post-transcriptional level (Gorski et al, 2017; Kunne et al, 2014)
We show that the RaiZ small noncoding RNAs (sRNAs) is induced upon entry in stationary phase and that it acts in trans to downregulate the translation of the hupA mRNA, which encodes the a-subunit of the bacterial histone-like protein HU
The cleavage site in the parental raiA mRNA that yields RaiZ is A/U-rich (Fig 1A), suggesting it would be a good substrate for the major mRNA processing enzyme RNase E (Mackie, 2013)
Summary
Many if not all organisms use small base-pairing RNAs to modulate mRNA expression at the post-transcriptional level (Gorski et al, 2017; Kunne et al, 2014) These regulatory pathways often rely upon a conserved RNA-binding protein, primary examples of which are Argonaute family members in the microRNA pathway of eukaryotes (Huntzinger & Izaurralde, 2011; Meister, 2013) and the Sm-like protein Hfq in prokaryotes (Bossi & Figueroa-Bossi, 2016; De Lay et al, 2013; Updegrove et al, 2016; Vogel & Luisi, 2011; Wagner & Romby, 2015). Intense work on these pathways over the past decade has revealed the existence of large post-transcriptional networks that affect almost every cellular aspect and rival the complexity of primary gene expression control at the level of transcription. Hfq only interacts with single-stranded regions of its ligands and, once the sRNA–mRNA duplex has been formed, it typically dissociates and is available to bind other sRNAs (Fender et al, 2010; Hopkins et al, 2011; Ishikawa et al, 2012)
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