Modulation of signal response by small RNAs through feed-forward loops

Abstract

In response to environmental changes, bacteria have evolved sophisticated regulatory networks that incorporate small RNAs (sRNAs) and transcription factors (TFs) to fine-tune cellular physiology. Both sRNAs and TFs modulate gene expression, but the former function via post-transcriptional mechanisms, while the latter act at the transcriptional level. However, it remains unclear why both regulatory layers are conserved through evolution, rather than one being sufficient. Here, we experimentally identified that CRP, a global regulator, regulates 25 small RNAs (sRNAs) in Escherichia coli. Interestingly, CRP also controls 80% of the target genes of these sRNAs. This architecture led us to identify 34 novel sRNA-mediated feed-forward loops (sFFLs)--circuits where CRP regulates both an sRNA and its target--within the CRP regulon. Quantitative PCR analysis of 16 such sFFLs revealed that each type possesses a distinct cAMP dose-response profile, suggesting that different sFFL structures embody unique regulatory logic. Specifically, coherent and incoherent type 3 and 4 sFFLs exhibit broader dynamic ranges in their dose-response compared to open-loop controls. Coherent and incoherent type 1 and 2 sFFLs appear more energy-efficient. Altogether, we propose that sRNAs cooperate with TFs through sFFLs to optimize both the energy efficiency and the diversity of signal response profiles. Therefore, sRNAs serve as critical components integrating transcriptional and post-transcriptional networks across diverse cellular pathways.