Abstract
Many RNA-RNA interactions depend on molecular chaperones to form and remain stable in living cells. A prime example is the RNA chaperone Hfq, which is a critical effector involved in regulatory interactions between small RNAs (sRNAs) and cognate target mRNAs in Enterobacteriaceae. While there is a great deal of in vitro biochemical evidence supporting the model that Hfq enhances rates or affinities of sRNA:mRNA interactions, there is little corroborating in vivo evidence. Here we used in vivo tools including reporter genes, co-purification assays, and super-resolution microscopy to analyze the role of Hfq in RyhB-mediated regulation, and we found that Hfq is often unnecessary for efficient RyhB:mRNA complex formation in vivo. Remarkably, our data suggest that a primary function of Hfq is to promote RyhB-induced cleavage of mRNA targets by RNase E. Moreover, our work indicates that Hfq plays a more limited role in dictating regulatory outcomes following sRNAs RybB and DsrA complex formation with specific target mRNAs. Our investigation helps evaluate the roles played by Hfq in some RNA-mediated regulation.
Highlights
Post-transcriptional regulation of gene expression by small regulatory RNAs is universally found in Bacteria, Archaea, and Eukarya [1,2,3]
We demonstrated that Hfq is recruited by the small RNAs (sRNAs) Spot42 to bind to the translation initiation region (TIR) of sdhC mRNA, thereby preventing the binding of 30S ribosomal subunit [34]
We monitored the effect of a ∆hfq mutation on RyhB sRNA [40] and its ability to interact with specific target mRNAs
Summary
Post-transcriptional regulation of gene expression by small regulatory RNAs (sRNAs) is universally found in Bacteria, Archaea, and Eukarya [1,2,3]. Bacterial sRNAs have been identified as crucial regulators that are often expressed to maintain the homeostasis of cellular pathways during environmental stress. These sRNAs are typically noncoding and smaller than 300 nucleotides. In Escherichia coli, ~100 sRNAs have been identified, encoded either on the chromosome or plasmids [1,4]. SRNAs act to negatively regulate target mRNAs by decreasing translation and/or increasing mRNA turnover. SRNA base-pairing with target mRNAs activates their translation [5,6,7,8]
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