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Journal of Bacteriology, January 2009, p. 461-476, Vol. 191, No. 2
0021-9193/09/$08.00+0     doi:10.1128/JB.01157-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

The Crp-Activated Small Noncoding Regulatory RNA CyaR (RyeE) Links Nutritional Status to Group Behavior{triangledown} ,{dagger}

Nicholas De Lay and Susan Gottesman*

Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892

Received 15 August 2008/ Accepted 26 October 2008

Small noncoding regulatory RNAs (sRNAs) play a key role in regulating the expression of many genes in Escherichia coli and other bacteria. Many of the sRNAs identified in E. coli bind to mRNAs in an Hfq-dependent manner and stimulate or inhibit translation of the mRNAs. Several sRNAs are regulated by well-studied global regulators. Here, we report characterization of the CyaR (RyeE) sRNA, which was previously identified in a global search for sRNAs in E. coli. We demonstrated that CyaR is positively regulated by the global regulator Crp under conditions in which cyclic AMP levels are high. We showed by using microarray analysis and Northern blotting that several genes are negatively regulated by CyaR, including ompX, encoding a major outer membrane protein; luxS, encoding the autoinducer-2 synthase; nadE, encoding an essential NAD synthetase; and yqaE, encoding a predicted membrane protein with an unknown function. Using translational lacZ fusions to yqaE, ompX, nadE, and luxS, we demonstrated that the negative regulation of these genes by CyaR occurs at the posttranscriptional level and is direct. Different portions of a highly conserved 3' region of CyaR are predicted to pair with sequences near the ribosome binding site of each of these targets; mutations in this sequence affected regulation, and compensatory mutations in the target mRNA restored regulation, confirming that there is direct regulation by the sRNA. These results provide insight into the mechanisms by which Crp negatively regulates genes such as luxS and ompX and provide a link between catabolite repression, quorum sensing, and nitrogen assimilation in E. coli.

* Corresponding author. Mailing address: Bldg. 37, Room 5132, Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892-4264. Phone: (301) 496-3524. Fax: (301) 496-3875. E-mail: susang{at}helix.nih.gov

{triangledown} Published ahead of print on 31 October 2008.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

Journal of Bacteriology, January 2009, p. 461-476, Vol. 191, No. 2
0021-9193/09/$08.00+0     doi:10.1128/JB.01157-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

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