A novel sRNA component of the carbon storage regulatory system of <i>Escherichia coli</i>

Weilbacher, Thomas; Suzuki, Kazushi; Dubey, Ashok Kumar; Wang, Xin; Gudapaty, Seshigirao; Morozov, Igor Y.; Baker, Carol S.; Georgellis, Dimitris; Babitzke, Paul; Romeo, Tony

doi:10.1046/j.1365-2958.2003.03459.x

Cited by 344 publications

(508 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: 91%

“…Furthermore, CsrA directly represses its own translation while indirectly activating its transcription (34). CsrA activity is antagonized by the noncoding small RNAs (sRNAs) CsrB and CsrC, which contain multiple CsrA binding sites that allow them to sequester this protein (35,36). Fluctuations in the levels of these RNAs regulate CsrA activity in response to the environment.…”

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confidence: 99%

“…Fluctuations in the levels of these RNAs regulate CsrA activity in response to the environment. 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).…”

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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: 91%

mentioning

confidence: 99%

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confidence: 99%

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

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“…The remaining sRNAs function by protein sequestration. Examples of sRNAs identified that regulate by this mechanism include CsrB, CsrC and 6S RNA (Liu et al, 1997;Wassarman & Storz, 2000;Weilbacher et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

Role of the sRNA GcvB in regulation of cycA in Escherichia coli

Pulvermacher

Stauffer

2009

Microbiology

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In Escherichia coli, the gcvB gene encodes a small non-translated RNA that regulates several genes involved in transport of amino acids and peptides (including sstT, oppA and dppA). Microarray analysis identified cycA as an additional regulatory target of GcvB. The cycA gene encodes a permease for the transport of glycine, d-alanine, d-serine and d-cycloserine. RT-PCR confirmed that GcvB and the Hfq protein negatively regulate cycA mRNA in cells grown in Luria–Bertani broth. In addition, deletion of the gcvB gene resulted in increased sensitivity to d-cycloserine, consistent with increased expression of cycA. A cycA : : lacZ translational fusion confirmed that GcvB negatively regulates cycA expression in Luria–Bertani broth and that Hfq is required for the GcvB effect. GcvB had no effect on cycA : : lacZ expression in glucose minimal medium supplemented with glycine. However, Hfq still negatively regulated the fusion in the absence of GcvB. A set of transcriptional fusions of cycA to lacZ identified a sequence in cycA necessary for regulation by GcvB. Analysis of GcvB identified a region complementary to this region of cycA mRNA. However, mutations predicted to disrupt base-pairing between cycA mRNA and GcvB did not alter expression of cycA : : lacZ. A model for GcvB function in cell physiology is discussed.

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RNA secondary structure prediction

Mathews

Zuker

2005

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

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This unit details the steps for predicting the secondary structure of an RNA sequence using free energy minimization (Mathews et al., 1999). Two protocols are given-one for the computer program RNAstructure (see Basic Protocol) and another for the mfold server (see Alternate Protocol). The mfold server is a World Wide Web adaptation of the mfold package for Unix computers. This package is available for use on Unix platforms and is described elsewhere (Zuker et al., 1999; http://www.rpi.edu/~zukerm/). RNAstructure is for personal computers (PCs) with Windows 95, Windows 98, or Windows NT. The mfold server is accessed via the Web using a standard browser (e.g., Microsoft Internet Explorer or Netscape Navigator). Both programs yield equivalent predictions. The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. In addition, a triangular plot called the energy dot plot that shows the superposition of all possible base pairs within a prescribed free energy increment is predicted. The choice of protocol is a matter of convenience for the user. RNAstructure requires a PC, whereas the mfold server requires accessing the software across the Internet. BASIC PROTOCOL This protocol lists the steps for structure prediction on a PC using the computer program RNAstructure. It assumes some basic familiarity with Windows. Materials Personal computer with Windows 95, Windows 98, or Windows NT (Microsoft) RNAstructure (free of charge at the Turner Lab Web site, http://rna.chem.rochester.edu) NOTE: It is recommended that a computer with a 100 MHz or faster processor be used. Also, memory use increases with the length of the sequence being analyzed; therefore

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A novel sRNA component of the carbon storage regulatory system of Escherichia coli

Abstract: Homologues of csrC are apparent in several Enterobacteriaceae. The regulatory and evolutionary implications of these findings are discussed.

Cited by 344 publications

References 51 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

Role of the sRNA GcvB in regulation of cycA in Escherichia coli

RNA secondary structure prediction

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