Cell 160, 228–240 (2015)

Bacteria such as Vibrio harveyi respond to changes in population density by regulating the expression of genes such as luxR that promote collective behaviors, including bioluminescence and biofilm formation. At low cell density, phosphorylation of the response regulator LuxO activates the transcription of the Qrr family of small regulatory RNAs (sRNAs). These sRNAs directly base pair with and thereby block the expression of mRNAs, including the quorum sensing regulators luxM, luxO and luxR. However, it was not known whether repression of the different mRNA targets occurs through identical or distinct regulatory mechanisms. To determine whether Qrr3 exhibits preference for particular target mRNAs, Feng et al. used an Escherichia coli competition assay expressing different combinations of target mRNAs encoding fluorescent tags in the presence of Qrr3 sRNA. They found that Qrr3 uses three distinct mechanisms to repress target gene expression. Base pairing of luxM mRNA with Qrr3 resulted in the coupled degradation of both mRNA and sRNA molecules, whereas base pairing of luxR mRNA to Qrr3 caused luxR but not the Qrr3 sRNA to be degraded. Finally, luxO binding to Qrr3 blocked LuxO protein production through Qrr3-mediated sequestration. Considering that luxM was known to bind the first and second stem loops of Qrr3 (SL1 and SL2) while luxR and luxO bind SL2, the specific base pairing patterns to Qrr3 might dictate the particular repression mechanism. Indeed, the authors found that modifying luxM mRNA to base pair only to SL2 blocked Qrr3 degradation, whereas modulating the binding strength of luxR or luxO mRNA to SL2 drove whether an mRNA was catalytically degraded or sequestered. Finally, mathematical modeling coupled with experiments showed that degradation of an mRNA target produced the highest level of immediate repression while sequestration provided the weakest and slowest rate of responsiveness and that these different mechanisms serve to control the dynamics and potency of quorum sensing.