The Base-Pairing RNA Spot 42 Participates in a Multioutput Feedforward Loop to Help Enact Catabolite Repression in Escherichia coli

SummaryBacteria selectively consume some carbon sources over others through a regulatory mechanism termed catabolite repression. Here, we show that the base-pairing RNA Spot 42 plays a broad role in catabolite repression in Escherichia coli by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse nonpreferred carbon sources. Many of the genes repressed by Spot 42 are transcriptionally activated by the global regulator CRP. Since CRP represses Spot 42, these regulators participate in a specific regulatory circuit called a multioutput feedforward loop. We found that this loop can reduce leaky expression of target genes in the presence of glucose and can maintain repression of target genes under changing nutrient conditions. Our results suggest that base-pairing RNAs in feedforward loops can help shape the steady-state levels and dynamics of gene expression.

Graphical AbstractFigure optionsDownload high-quality image (250 K)Download as PowerPoint slideHighlights
► Spot 42 regulates the consumption of numerous nonpreferred carbon sources
► Spot 42 participates with CRP in a multioutput coherent feedforward loop
► The loop can reduce the leaky expression of glucose-repressed genes
► The loop can help maintain glucose repression under changing nutrient conditions