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Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation

Nature Structural & Molecular Biology volume 16, pages 840–846 (2009)Cite this article

Abstract

Bacterial small noncoding RNAs (sRNAs) generally recognize target mRNAs in the 5′ region to prevent 30S ribosomes from initiating translation. It was thought that the mRNA coding sequence (CDS) was refractory to sRNA-mediated repression, because elongating 70S ribosomes have an efficient RNA helicase activity that prevents stable target pairing. We report that the Hfq-associated MicC sRNA silences Salmonella typhimurium ompD mRNA via a ≤12-bp RNA duplex within the CDS (codons 23–26) that is essential and sufficient for repression. MicC does not inhibit translational initiation at this downstream position but instead acts by accelerating RNase E–dependent ompD mRNA decay. We propose an alternative gene-silencing pathway within bacterial CDS wherein sRNAs repress targets by endonucleolytic mRNA destabilization rather than by the prototypical inhibition of translational initiation. The discovery of CDS targeting markedly expands the sequence space for sRNA target predictions in bacteria.

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Figure 1: MicC sRNA and its expression in Salmonella.
Figure 2: MicC sRNA targets both the ompC and the ompD mRNAs of Salmonella.
Figure 3: Analysis of the MicC-ompD RNA interaction in vitro and in vivo.
Figure 4: Validation of the MicC-ompD interaction in vivo.
Figure 5: MicC binding does not interfere with ompD mRNA translation in vitro.
Figure 6: RNase E is essential for ompD repression by MicC.

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Acknowledgements

We thank G.A. Mackie and B. Luisi for insightful comments on the manuscript and E. Bär for technical assistance. We are grateful for materials from S. Kushner (University of Georgia, E. coli strains), R. Misra (Arizona State University, porin antiserum) and K. Nierhaus (Max Planck Institute for Molecular Genetics, Berlin, 30S ribosomes). This work was supported by a Boehringer Ingelheim Fonds stipend to K.P., by the Biotechnology and Biological Sciences Research Council Core Strategic Grant to J.C.D.H. and by funds of the Deutsche Forschungsgemeinschaft Priority Program SPP1258 Sensory and Regulatory RNAs in Prokaryotes to J.V.

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Authors and Affiliations

  1. Max Planck Institute for Infection Biology, RNA Biology Group, Berlin, Germany

    Verena Pfeiffer, Kai Papenfort & Jörg Vogel

  2. Institute of Food Research, Norwich, UK

    Sacha Lucchini & Jay C D Hinton

  3. Deparment of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Ireland

    Jay C D Hinton

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  1. Verena Pfeiffer
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  2. Kai Papenfort
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Contributions

V.P. and J.V. designed the research; V.P. performed all but the transcriptomic experiments; K.P. and S.L. conducted and analyzed the transcriptomic experiments; J.V. and J.C.D.H. wrote the manuscript, which all authors commented on; J.V. supervised the project.

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Correspondence to Jörg Vogel.

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Pfeiffer, V., Papenfort, K., Lucchini, S. et al. Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 16, 840–846 (2009). https://doi.org/10.1038/nsmb.1631

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