It is not clear how Hfq prioritizes the different RNAs, or how binding to Hfq alters RNA regulation. However, it is outnumbered by the many different RNA molecules in the cell, which compete for binding to the protein. It is critical for bacterial growth under harsh conditions and it is involved in the process through which pathogenic bacteria infect cells. Certain bacterial RNA-binding proteins, such as Hfq, protect sRNAs from being degraded, and help them find their mRNA targets. Each sRNA can bind to several specific mRNA targets, and lead to their degradation by an enzyme called RNase E. Bacteria can regulate their levels of mRNA molecules, and they can therefore control how many proteins are being made, by producing a different type of RNA called small regulatory RNAs or sRNAs. Messenger RNAs or mRNAs are molecules that the cell uses to transfer the information stored in the cell’s DNA so it can be used to make proteins. Finally, our data suggest that binding of Hfq to certain mRNAs through its distal face can recruit RNase E to promote turnover of these mRNAs in a sRNA-independent manner, and such regulatory function of Hfq can be decoyed by sRNA competitors that bind strongly at the distal face. In addition, sRNAs can either co-occupy Hfq with the mRNA as a ternary complex, or displace the mRNA from Hfq in a binding face-dependent manner, suggesting mechanisms through which sRNAs rapidly access Hfq to induce sRNA-mediated gene regulation. We demonstrate that under normal growth conditions, Hfq exhibits widespread mRNA-binding activity, with the distal face of Hfq contributing mostly to the mRNA binding in vivo. Using live-cell super-resolution imaging, we can distinguish Hfq binding to different sizes of cellular RNAs. In bacteria, the RNA chaperone Hfq is an important post-transcriptional gene regulator. RNA-binding proteins play myriad roles in regulating RNAs and RNA-mediated functions.
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