Translational activation by the noncoding RNA DsrA involves alternative RNase III processing in the rpoS 5′-leader

Armin Resch; Taras Afonyushkin; Tania B. Lombo; Kenneth J. McDowall; Udo Bläsi; Vladimir R. Kaberdin

doi:10.1261/rna.603108

Translational activation by the noncoding RNA DsrA involves alternative RNase III processing in the rpoS 5′-leader

¹Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, A-1030 Vienna, Austria
²Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom

↵3 These authors equally contributed to this work.

Abstract

The intricate regulation of the Escherichia coli rpoS gene, which encodes the stationary phase sigma-factor σ^S, includes translational activation by the noncoding RNA DsrA. We observed that the stability of rpoS mRNA, and concomitantly the concentration of σ^S, were significantly higher in an RNase III-deficient mutant. As no decay intermediates corresponding to the in vitro mapped RNase III cleavage site in the rpoS leader could be detected in vivo, the initial RNase III cleavage appears to be decisive for the observed rapid inactivation of rpoS mRNA. In contrast, we show that base-pairing of DsrA with the rpoS leader creates an alternative RNase III cleavage site within the rpoS/DsrA duplex. This study provides new insights into regulation by small regulatory RNAs in that the molecular function of DsrA not only facilitates ribosome loading on rpoS mRNA, but additionally involves an alternative processing of the target.

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Footnotes

Reprint requests to: Vladimir R. Kaberdin, Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, Dr. Bohrgasse 9/4, A-1030 Vienna, Austria; e-mail: vladimir.kaberdin{at}univie.ac.at; fax: 43-1-4277-9546.
Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.603108.
- Received April 23, 2007.
- Accepted November 9, 2007.