Differential Regulation of CsrC and CsrB by CRP-cAMP in Salmonella enterica

Abstract

Post-transcriptional regulation mediated by regulatory small RNAs (sRNAs) has risen as a key player in fine-tuning gene expression in response to environmental stimuli. Here, we show that, in Salmonella enterica , the central metabolic regulator CRP-cAMP differentially regulates the sRNAs CsrB and CsrC in a growth phase-dependent manner. While CsrB expression remains unchanged during growth, CsrC displays a growth phase-dependent expression profile, being weakly expressed at the logarithmic growth phase and induced upon entry into stationary phase. We show that CRP-cAMP contributes to the expression pattern of CsrC by repressing its expression during the logarithmic growth phase. The CRP-cAMP mediated repression of CsrC is independent of SirA, a known transcriptional CsrB/CsrC activator. We further show that the sRNA Spot 42, which is derepressed in a Δ crp strain, upregulates CsrC during logarithmic growth. We propose a model where the growth-dependent regulation of CsrC is sustained by the CRP-cAMP-mediated repression of Spot 42. Together, our data point toward a differential regulation of the sRNAs CsrB and CsrC in response to environmental stimuli, leading to fine-tuning of gene expression via the sequestration of the RNA-binding protein CsrA.

A small RNA derived from the 5’ end of the IS200tnpAtranscript regulates multiple virulence regulons inSalmonellaTyphimurium

“…The larger increase in differential expression of CsrC relative to CsrB in the Δ 5’tnpA strain is suggestive of reduced expression/activity of Crp-cAMP in this strain because Crp-cAMP specifically inhibits CsrC expression early in growth 21 . We also considered this possibility because of our finding from RNA-seq that the phsABC operon is the most downregulated set of genes in the Δ 5’tnpA strain; earlier published data showed that phsABC operon expression is subject to catabolite repression 42 .…”

“…Based on the known functions of CsrC, Spot 42 and LrhA, it is straightforward to model the additive impact of altered regulation of these respective genes on hilD expression. The increase in Spot 42 levels would increase the amount of hilD transcript through Spot 42 binding to the 3’UTR of hilD 21 . The increase in CsrC (and possibly CsrB) levels would increase the amount of hilD translation by titrating CsrA.…”

“…For example, sRNAs CsrB and CsrC compete with other RNAs for binding the global translational repressor CsrA, effectively titrating CsrA protein, relieving hilD repression [17][18][19] . Transcription of csrB and csrC is turned on by the TF SirA and negatively regulated by Crp-cAMP 20,21 . Spot 42 (encoded by spf) is another sRNA which impinges on hilD expression.…”

Small RNAs, Large Networks: Posttranscriptional Regulons in Gram-Negative Bacteria

“…Specifically, CsrA binds to and protects Spot 42 from ribonucleolytic decay by RNase E and thereby enhances target mRNA repression (66). Given that CsrA activity is also controlled by CRP (30), one can speculate that Spot 42 and CsrA together modulate the overall output of the CRP regulon at the RNA level. In fact, in pathogenic microorganisms, such as S. enterica, CRP in concert with cAMP has been shown to inhibit virulence gene expression through a posttranscriptional mechanism (31).…”