Different csrA Expression Levels in C versus K-12 E. coli Strains Affect Biofilm Formation and Impact the Regulatory Mechanism Presided by the CsrB and CsrC Small RNAs

Abstract

Escherichia coli C is a strong biofilm producer in comparison to E. coli K-12 laboratory strains due to higher expression of the pgaABCD operon encoding the enzymes for the biosynthesis of the extracellular polysaccharide poly-β-1,6-N-acetylglucosamine (PNAG). The pgaABCD operon is negatively regulated at the post-transcriptional level by two factors, namely CsrA, a conserved RNA-binding protein controlling multiple pathways, and the RNA exonuclease polynucleotide phosphorylase (PNPase). In this work, we investigated the molecular bases of different PNAG production in C-1a and MG1655 strains taken as representative of E. coli C and K-12 strains, respectively. We found that pgaABCD operon expression is significantly lower in MG1655 than in C-1a; consistently, CsrA protein levels were much higher in MG1655. In contrast, we show that the negative effect exerted by PNPase on pgaABCD expression is much stronger in C-1a than in MG1655. The amount of CsrA and of the small RNAs CsrB, CsrC, and McaS sRNAs regulating CsrA activity is dramatically different in the two strains, whereas PNPase level is similar. Finally, the compensatory regulation acting between CsrB and CsrC in MG1655 does not occur in E. coli C. Our results suggest that PNPase preserves CsrA-dependent regulation by indirectly modulating csrA expression.

Regulation of biofilm formation by non-coding RNA in prokaryotes

“…CsrA, the global carbon storage regulator, is also a regulator of biofilm formation, which is controlled at the level of transcription and post-transcriptionally, both by indirect and direct mechanisms ( Jackson et al., 2002 ; Mitra et al., 2013 ). Two small ncRNA, namely, CsrB and CsrC, bind to CsrA and sequester its activity ( Carzaniga et al., 2021 ).…”

The role of RNA regulators, quorum sensing and c‐di‐GMP in bacterial biofilm formation

“…The Csr regulatory system is highly conserved among many pathogenic bacteria, including Pseudomonas aeruginosa , Salmonella Typhimurium and Yersinia pseudotuberculosis, where it controls biofilm formation and virulence mechanisms [ 33 , 34 , 35 ]. Surprisingly, a recent study comparing E. coli C and E. coli K12 discovered that the levels of CsrB and CsrC are much higher in the K12 strain than in the C strain [ 36 ]. This is an apparent contradiction, since E. coli C is naturally much more prone to produce biofilms than the E. coli K12 strains and, as such, it would be expected that the levels of these sRNAs would be higher in the C strain.…”

“…This is an apparent contradiction, since E. coli C is naturally much more prone to produce biofilms than the E. coli K12 strains and, as such, it would be expected that the levels of these sRNAs would be higher in the C strain. In fact, the authors found that in E. coli C, there is no compensatory regulation similar to the one that exists between CsrB and CsrC in E. coli K12 strains [ 36 ]. This difference between two E. coli strains is a clear example that although the same systems are conserved among bacteria it should not be assumed that their function is equal.…”

A linear and circular dual-conformation noncoding RNA involves in oxidative stress tolerance of Bacillus altitudinis

“…This base pairing alters mRNA stability or translation, thus results in inhibition or activation of target gene expression. Nonetheless, there are some sRNAs act through interactions with regulatory proteins directly, e.g., the RNA component of the ubiquitous signal recognition particle (SRP), and sRNA CsrB/CsrC that sequester small protein CsrA [3][4][5] . Up to now, all of the bacterial noncoding RNAs are reported functioning through linear forms.…”