Regulatory Circuitry of the CsrA/CsrB and BarA/UvrY Systems of<i>Escherichia coli</i>

Suzuki, Kazushi; Wang, Xin; Weilbacher, Thomas; Pernestig, Anna-Karin; Melefors, Öjar; Georgellis, Dimitris; Babitzke, Paul; Romeo, Tony

doi:10.1128/jb.184.18.5130-5140.2002

Cited by 256 publications

(354 citation statements)

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“…Normal transcription of both csrB and csrC depends on P-UvrY, although csrB transcription is more highly dependent than that of csrC (3,36,38). In addition, the RNA helicase DeaD activates UvrY translation, which then activates csrB/C transcription (62).…”

Section: Resultsmentioning

confidence: 99%

“…Although we were unable to detect expression of csrB or csrC using in vitro transcription reactions with purified components (data not shown), P-UvrY was previously found to directly activate the expression of csrB-lacZ and csrC-lacZ transcriptional fusions in S-30 transcription-translation assays (36,38). Thus, we used the latter approach to determine if cAMP-CRP directly represses expression from the csrC-lacZ transcriptional fusion in the plasmid pLFXcsrC-lacZ.…”

Section: Fig 2 Effects Of Camp-crp On Csrb and Csrc Levels And Decay mentioning

confidence: 92%

“…Coupled transcriptiontranslational assays for expression of pLFXcsrC-lacZ were performed with S-30 extracts prepared from a uvrY-deficient strain (CF7789 uvrY::cam) as described previously (38,61), except that the reaction mixtures were assembled to reach 32 l and contained 0.5 U E. coli RNA polymerase holoenzyme and 3 l of [ 35 S]methionine (1,175 Ci/mmol). Radiolabeled proteins were separated by electrophoresis through Bis-Tris SDS-PAGE.…”

Section: Methodsmentioning

confidence: 99%

“…Transcription of both csrB and csrC (csrB/C) is activated by the BarA-UvrY two-component signal transduction system (TCS) in response to carboxylic acids such as formate and acetate (3,(36)(37)(38)(39)(40)(41). CsrA indirectly activates transcription of CsrB and CsrC through its effects on BarA-UvrY, creating a negative-feedback loop within the Csr circuitry (37,38,42). CsrB/C turnover requires the GGDEF-EAL domain protein CsrD, which is necessary for cleavage by RNase E and turnover (42,43).…”

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confidence: 99%

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Circuitry Linking the Catabolite Repression and Csr Global Regulatory Systems of Escherichia coli

et al. 2016

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Cyclic AMP (cAMP) and the cAMP receptor protein (cAMP-CRP) and CsrA are the principal regulators of the catabolite repression and carbon storage global regulatory systems, respectively. cAMP-CRP controls the transcription of genes for carbohydrate metabolism and other processes in response to carbon nutritional status, while CsrA binds to diverse mRNAs and regulates translation, RNA stability, and/or transcription elongation. CsrA also binds to the regulatory small RNAs (sRNAs) CsrB and CsrC, which antagonize its activity. The BarA-UvrY two-component signal transduction system (TCS) directly activates csrB and csrC (csrB/C) transcription, while CsrA does so indirectly. We show that cAMP-CRP inhibits csrB/C transcription without negatively regulating phosphorylated UvrY (P-UvrY) or CsrA levels. A crp deletion caused an elevation in CsrB/C levels in the stationary phase of growth and increased the expression of csrB-lacZ and csrClacZ transcriptional fusions, although modest stimulation of CsrB/C turnover by the crp deletion partially masked the former effects. DNase I footprinting and other studies demonstrated that cAMP-CRP bound specifically to three sites located upstream from the csrC promoter, two of which overlapped the P-UvrY binding site. These two proteins competed for binding at the overlapping sites. In vitro transcription-translation experiments confirmed direct repression of csrC-lacZ expression by cAMP-CRP. In contrast, cAMP-CRP effects on csrB transcription may be mediated indirectly, as it bound nonspecifically to csrB DNA. In the reciprocal direction, CsrA bound to crp mRNA with high affinity and specificity and yet exhibited only modest, conditional effects on expression. Our findings are incorporated into an emerging model for the response of Csr circuitry to carbon nutritional status. IMPORTANCECsr (Rsm) noncoding small RNAs (sRNAs) CsrB and CsrC of Escherichia coli use molecular mimicry to sequester the RNA binding protein CsrA (RsmA) away from lower-affinity mRNA targets, thus eliciting major shifts in the bacterial lifestyle. CsrB/C transcription and turnover are activated by carbon metabolism products (e.g., formate and acetate) and by a preferred carbon source (glucose), respectively. We show that cAMP-CRP, a mediator of classical catabolite repression, inhibits csrC transcription by binding to the upstream region of this gene and also inhibits csrB transcription, apparently indirectly. We propose that glucose availability activates pathways for both synthesis and turnover of CsrB/C, thus shaping the dynamics of global signaling in response to the nutritional environment by poising CsrB/C sRNA levels for rapid response.T he Csr (carbon storage regulator) or Rsm (repressor of stationary-phase metabolites) system is a widely conserved bacterial posttranscriptional regulatory system (1-3). Its components, their functions, and the mechanisms by which the central regulator of this system, CsrA or RsmA, affects gene expression have been studied primarily in Gammaproteobacteria (4-6). The...

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Section: Resultsmentioning

confidence: 99%

Section: Fig 2 Effects Of Camp-crp On Csrb and Csrc Levels And Decay mentioning

confidence: 92%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Circuitry Linking the Catabolite Repression and Csr Global Regulatory Systems of Escherichia coli

et al. 2016

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“…Interestingly, the Rcs regulon includes paralogues of UvrY and BolA. In E. coli, the BarA/UvrY two-component regulatory system can activate biofilm formation, and ectopic expression of UvrY stimulated biofilm formation (Suzuki et al, 2002). Overproduction of BolA in E. coli induces biofilm development, while BolA deletion decreases biofilms (Vieira et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

The importance of the Rcs phosphorelay in the survival and pathogenesis of the enteropathogenic yersiniae

et al. 2008

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Different combinations of atomic interactions predict protein‐small molecule and protein‐DNA/RNA affinities with similar accuracy

Dias

Kolazckowski

2015

Proteins

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Interactions between proteins and other molecules play essential roles in all biological processes. Although it is widely held that a protein's ligand specificity is determined primarily by its three‐dimensional structure, the general principles by which structure determines ligand binding remain poorly understood. Here we use statistical analyses of a large number of protein−ligand complexes with associated binding‐affinity measurements to quantitatively characterize how combinations of atomic interactions contribute to ligand affinity. We find that there are significant differences in how atomic interactions determine ligand affinity for proteins that bind small chemical ligands, those that bind DNA/RNA and those that interact with other proteins. Although protein‐small molecule and protein‐DNA/RNA binding affinities can be accurately predicted from structural data, models predicting one type of interaction perform poorly on the others. Additionally, the particular combinations of atomic interactions required to predict binding affinity differed between small‐molecule and DNA/RNA data sets, consistent with the conclusion that the structural bases determining ligand affinity differ among interaction types. In contrast to what we observed for small‐molecule and DNA/RNA interactions, no statistical models were capable of predicting protein−protein affinity with >60% correlation. We demonstrate the potential usefulness of protein‐DNA/RNA binding prediction as a possible tool for high‐throughput virtual screening to guide laboratory investigations, suggesting that quantitative characterization of diverse molecular interactions may have practical applications as well as fundamentally advancing our understanding of how molecular structure translates into function. Proteins 2015; 83:2100–2114. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

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Regulatory Circuitry of the CsrA/CsrB and BarA/UvrY Systems ofEscherichia coli

Cited by 256 publications

References 59 publications

Circuitry Linking the Catabolite Repression and Csr Global Regulatory Systems of Escherichia coli

Circuitry Linking the Catabolite Repression and Csr Global Regulatory Systems of Escherichia coli

The importance of the Rcs phosphorelay in the survival and pathogenesis of the enteropathogenic yersiniae

Different combinations of atomic interactions predict protein‐small molecule and protein‐DNA/RNA affinities with similar accuracy

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