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J. Biol. Chem., Vol. 283, Issue 19, 13289-13301, May 9, 2008

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S1 Ribosomal Protein Functions in Translation Initiation and Ribonuclease RegB Activation Are Mediated by Similar RNA-Protein Interactions

AN NMR AND SAXS ANALYSIS^*

Pascale Aliprandi, Christina Sizun, Javier Perez, Fabien Mareuil, Sandrine Caputo, Jean-Louis Leroy^¶, Benoît Odaert¹, Soumaya Laalami^||**, Marc Uzan^||**, and François Bontems²

From the CNRS, Antenne de l'ICSN (UPR2301) à l'Ecole Polytechnique, Ecole Polytechnique, 91128 Palaiseau, France, SWING, Synchrotron SOLEIL, L'Orme des Merisiers, BP48 Saint-Aubin, 91192 Gif-sur-Yvette, France, ^¶CNRS, Laboratoire de Chimie et Biologie Structurale, ICSN (UPR2301), Avenue de la Terrasse, 91190 Gif-sur-Yvette, France, ^||Université Paris VI et VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris cedex 05, France, and the ^**CNRS, UMR7592, Institut Jacques Monod, 2 place Jussieu, 75251 Paris cedex 05, France

The ribosomal protein S1, in Escherichia coli, is necessary for the recognition by the ribosome of the translation initiation codon of most messenger RNAs. It also participates in other functions. In particular, it stimulates the T4 endoribonuclease RegB, which inactivates some of the phage mRNAs, when their translation is no longer required, by cleaving them in the middle of their Shine-Dalgarno sequence. In each function, S1 seems to target very different RNAs, which led to the hypothesis that it possesses different RNA-binding sites. We previously demonstrated that the ability of S1 to activate RegB is carried by a fragment of the protein formed of three consecutive domains (domains D3, D4, and D5). The same fragment plays a central role in all other functions. We analyzed its structural organization and its interactions with three RNAs: two RegB substrates and a translation initiation region. We show that these three RNAs bind the same area of the protein through a set of systematic (common to the three RNAs) and specific (RNA-dependent) interactions. We also show that, in the absence of RNA, the D4 and D5 domains are associated, whereas the D3 and D4 domains are in equilibrium between open (noninteracting) and closed (weakly interacting) forms and that RNA binding induces a structural reorganization of the fragment. All of these results suggest that the ability of S1 to recognize different RNAs results from a high adaptability of both its structure and its binding surface.

Received for publication, August 24, 2007 , and in revised form, January 18, 2008.

^* This work was supported by a grant from ICSN (UPR2301, CNRS) (to P. A., F. M., S. C., and B. O.) and by the SAXIER Project Sixth Framework Programme (to J. P.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1-S3.

¹ Present address: Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France.

² To whom correspondence should be addressed: ICSN, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France. Tel.: 33-1-69-82-36-78; E-mail: Francois.Bontems{at}icsn.cnrs-gif.fr.

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