The roles of small RNAs in regulatory networks

The ongoing characterization of base pairing small RNAs (sRNAs) in bacteria has started to reveal how these sRNAs participate in gene regulatory networks. As an example, we have found 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. We suggest that base pairing sRNAs help shape the steady-state levels and dynamics of gene expression in many regulatory networks.