Structural basis of the non-coding RNA RsmZ acting as a protein sponge

Olivier Duss, Erich Michel, Maxim Yulikov, Mario Schubert, Gunnar Jeschke and Frédéric H.-T. Allain ()
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Olivier Duss: Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
Erich Michel: Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
Maxim Yulikov: Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
Mario Schubert: Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
Gunnar Jeschke: Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
Frédéric H.-T. Allain: Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland

Nature, 2014, vol. 509, issue 7502, 588-592

Abstract: Abstract MicroRNA and protein sequestration by non-coding RNAs (ncRNAs) has recently generated much interest. In the bacterial Csr/Rsm system, which is considered to be the most general global post-transcriptional regulatory system responsible for bacterial virulence, ncRNAs such as CsrB or RsmZ activate translation initiation by sequestering homodimeric CsrA-type proteins from the ribosome-binding site of a subset of messenger RNAs. However, the mechanism of ncRNA-mediated protein sequestration is not understood at the molecular level. Here we show for Pseudomonas fluorescens that RsmE protein dimers assemble sequentially, specifically and cooperatively onto the ncRNA RsmZ within a narrow affinity range. This assembly yields two different native ribonucleoprotein structures. Using a powerful combination of nuclear magnetic resonance and electron paramagnetic resonance spectroscopy we elucidate these 70-kilodalton solution structures, thereby revealing the molecular mechanism of the sequestration process and how RsmE binding protects the ncRNA from RNase E degradation. Overall, our findings suggest that RsmZ is well-tuned to sequester, store and release RsmE and therefore can be viewed as an ideal protein ‘sponge’.

Date: 2014
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DOI: 10.1038/nature13271

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