Post-transcriptional regulation on a global scale: form and function of Csr/Rsm systems

Abstract

Originally described as a repressor of gene expression in the stationary phase of growth, CsrA (RsmA) regulates primary and secondary metabolic pathways, biofilm formation, motility, virulence circuitry of pathogens, quorum sensing and stress response systems by binding to conserved sequences in its target mRNAs and altering their translation and/or turnover. While the binding of CsrA to RNA is understood at an atomic level, new mechanisms of gene activation and repression by this protein are still emerging. In the γ-proteobacteria, small non-coding RNAs (sRNAs) use molecular mimicry to sequester multiple CsrA dimers away from mRNA. In contrast, the FliW protein of Bacillus subtilis inhibits CsrA activity by binding to this protein, thereby establishing a checkpoint in flagellum morphogenesis. Turnover of CsrB and CsrC sRNAs in Escherichia coli requires a specificity protein of the GGDEF-EAL domain superfamily, CsrD, in addition to the housekeeping nucleases RNase E and PNPase. The Csr system of E. coli contains extensive autoregulatory circuitry, which governs the expression and activity of CsrA. Interaction of the Csr system with transcriptional regulatory networks results in a variety of complex response patterns. This minireview will highlight basic principles and new insights into the workings of these complex eubacterial regulatory systems.

Fig. 1

Outline of the E. coli Csr system. Binding of the CsrA dimer to an mRNA can block translation (shown), destabilize, or stabilize the mRNA. Noncoding RNAs (CsrB and CsrC) containing multiple CsrA binding sites within the loops of predicted stem-loops compete with mRNAs for CsrA binding, thus antagonizing CsrA activity. Free CsrA is regenerated by the turnover of CsrB/C RNAs, which requires RNase E, polynucleotide phosphorylase (PNPase) and CsrD, an atypical GGDEF-EAL domain protein.

Fig. 2

Autoregulatory loops of the Csr system. CsrA binds to its own mRNA and inhibits translation initiation. It also indirectly activates its own transcription at P3, an RpoS-dependent promoter. CsrA also activates the expression of its two RNA antagonists, CsrB and CsrC, via the BarA-UvrY two-component signal transduction system. Phosphorylated UvrY directly activates transcription of csrB and csrC. The sRNAs CsrB and CsrC contain several CsrA binding sites such that each sRNA is capable of sequestering several CsrA dimers. CsrA modestly represses expression of CsrD, a protein that is required for degradation of CsrB and CsrC by RNase E and PNPase (from Yakhnin et al., 2011).

Fig 3

Interactions of the Csr system with other E. coli regulatory systems shape diverse circuitry. A. CsrA posttranscriptionally represses several steps in the synthesis of the biofilm polysaccharide β-1,6-N-acetylglucosamine, tightening the regulation of biofilm formation. (from Pannuri et al. 2011). B. The Csr and stringent response systems interact to reinforce transcriptional control by ppGpp, as well as relieve repression of relA and ppGpp synthesis by CsrA during the stringent response (from Edwards et al. 2011). C. Expression of pathogenicity genes in the Lee locus is compromised by both low and high activity of CsrA due to its opposing effects on structural genes and the GrlA regulator (Bhatt et al. 2009). The effect of CsrA on escD (?) is indirect.

Fig 4

A partner-switching mechanism involving B. subtilis CsrA, FliW and Hag proteins create a morphogenetic checkpoint for flagellum biosynthesis. CsrA protein represses translation of hag mRNA encoding flagellin. FliW competitively binds to Hag or CsrA, depending on the intracellular concentration of Hag. Prior to the completion of the flagellum secretion channel or upon capping of the pore, high intracellular levels of Hag occupy FliW and CsrA is free to block Hag translation. When the flagellum channel is open and Hag protein is being actively secreted, intracellular Hag levels drop and FliW is free to bind to CsrA, derepressing the synthesis of Hag protein (Mukherjee et al., 2011).