Small Regulatory RNAs in the Control of Motility and Biofilm Formation in E. coli and Salmonella

Abstract

Biofilm formation in Escherichia coli and other enteric bacteria involves the inverse regulation of the synthesis of flagella and biofilm matrix components such as amyloid curli fibres, cellulose, colanic acid and poly-N-acetylglucosamine (PGA). Physiologically, these processes reflect the transition from growth to stationary phase. At the molecular level, they are tightly controlled by various sigma factors competing for RNA polymerase, a series of transcription factors acting in hierarchical regulatory cascades and several nucleotide messengers, including cyclic-di-GMP. In addition, a surprisingly large number of small regulatory RNAs (sRNAs) have been shown to directly or indirectly modulate motility and/or biofilm formation. This review aims at giving an overview of these sRNA regulators and their impact in biofilm formation in E. coli and Salmonella. Special emphasis will be put on sRNAs, that have known targets such as the mRNAs of the flagellar master regulator FlhDC, the stationary phase sigma factor σS (RpoS) and the key biofilm regulator CsgD that have recently been shown to act as major hubs for regulation by multiple sRNAs.

Figure 1

Motility and biofilm control networks in E. coli. (A) Transcriptional network, that controls switching between motility and biofilm formation. (B) sRNA network, that controls motility and biofilm formation at the mRNA level. Regulatory effects within the transcriptional network (grey arrows) are shown only in part due to space constraints. For distinct regulatory motifs and their function within the entire network, see Figure 3. Blue boxes: targets with “hub” mRNAs/proteins; grey rectangles: transcription factors; pentagon: c-di-GMP-binding effector protein; red boxes: c-di-GMP signaling modules (red letters: diguanylate cyclase, blue letters: phosphodiesterase); green ovals: sRNAs; dotted lines: indirect effects; straight lines: direct effects.

Figure 2

“hub” mRNAs—secondary structures of relevant 5′UTR parts and sRNA binding sites. (A) Structure prediction of flhD 5′UTR [61]. (B) Predicted and mapped structure of rpoS 5′UTR [74] (C) Predicted and mapped structure of csgD 5′UTR [75]. sRNA binding sites were computationally predicted and proven by compensatory basepair exchanges (all except GcvB) [,–,,–77] or mapped [64,75]. Positions on the mRNA sequence are numbered according to the transcriptional start site. Bold nucleotides: coding region; black box: start codon; red box: Shine Dalgarno Sequence; colored bars: sRNA binding sites; blue nucleotides: unfolded stem loop structures.

Figure 3

Regulatory sRNA control modules can be grouped into 4 classes according to their regulatory output with respect to expression of flagella and biofilm components. For an explanation of the symbols, see legend of Figure 1. Grey arrows: shown in Salmonella only.