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Journal of Bacteriology, September 2009, p. 5446-5457, Vol. 191, No. 17
0021-9193/09/$08.00+0     doi:10.1128/JB.00602-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

CodY Activates Transcription of a Small RNA in Bacillus subtilis{triangledown} ,{dagger}

Heike Preis, Rita A. Eckart, Rajani K. Gudipati,{ddagger} Nadja Heidrich,§ and Sabine Brantl*

Friedrich-Schiller-Universität Jena, Biologisch-Pharmazeutische Fakultät, AG Bakteriengenetik, Philosophenweg 12, Jena D-07743, Germany

Received 8 May 2009/ Accepted 16 June 2009

Regulatory small RNAs (sRNAs) in bacterial genomes have become a focus of research over the past 8 years. Whereas more than 100 such sRNAs have been found in Escherichia coli, relatively little is known about sRNAs in gram-positive bacteria. Using a computational approach, we identified two sRNAs in intergenic regions of the Bacillus subtilis genome, SR1 and SR2 (renamed BsrF). Recently, we demonstrated that SR1 inhibits the translation initiation of the transcriptional activator AhrC. Here, we describe detection of BsrF, its expression profile, and its regulation by CodY. Furthermore, we mapped the secondary structure of BsrF. BsrF is expressed in complex and minimal media in all growth phases in B. subtilis and, with a similar expression profile, also in Bacillus amyloliquefaciens. Neither overexpression nor deletion of bsrF affected the growth of B. subtilis. BsrF was found to be long-lived in complex and minimal media. Analysis of 13 putative transcription factor binding sites upstream of bsrF revealed only an effect for CodY. Here, we showed by using Northern blotting, lacZ reporter gene fusions, in vitro transcription, and DNase I footprinting that the transcription of bsrF is activated by CodY in the presence of branched-chain amino acids and GTP. Furthermore, BsrF transcription was increased 1.5- to 2-fold by glucose in the presence of branched-chain amino acids, and this increase was independent of the known glucose-dependent regulators. BsrF is the second target for which transcriptional activation by CodY has been discovered.

* Corresponding author. Mailing address: Friedrich-Schiller-Universität Jena, Biologisch-Pharmazeutische Fakultät, AG Bakteriengenetik, Philosophenweg 12, Jena D-07743, Germany. Phone: 49-3641-949570. E-mail: Sabine.Brantl{at}uni-jena.de

{triangledown} Published ahead of print on 19 June 2009.

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

{ddagger} Present address: Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, France.

§ Present address: Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, S-75124 Uppsala, Sweden.

Journal of Bacteriology, September 2009, p. 5446-5457, Vol. 191, No. 17
0021-9193/09/$08.00+0     doi:10.1128/JB.00602-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



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