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Nucleic Acids Research Advance Access published online on July 15, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp547
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Probing the relationship between Gram-negative and Gram-positive S1 proteins by sequence analysis

Philippe Salah1, Marco Bisaglia1,4, Pascale Aliprandi1, Marc Uzan2,3, Christina Sizun1 and François Bontems1,*

1CNRS, Centre de Recherche CNRS de Gif-sur-Yvette (FRC 3115), Institut de Chimie des Substances Naturelles, avenue de la terrasse, 91198 Gif-sur-Yvette Cedex, 2Université Paris 6-Pierre et Marie Curie, 4 place Jussieu, 75252 Paris cedex 05, 3CNRS, FRE3207 Acides Nucléiques et Biophotonique, 4 place Jussieu, 75251 Paris cedex 05, France and 4Department of Biology, University of Padova, via U. Bassi 58/B 35121 Padova, Italia

*To whom correspondence should be addressed. Tel: +(33) 1 69 82 36 78; Email: francois.bontems{at}icsn.cnrs-gif.fr

Received April 10, 2009. Revised May 19, 2009. Accepted June 10, 2009.

Escherichia coli ribosomal protein S1 is required for the translation initiation of messenger RNAs, in particular when their Shine–Dalgarno sequence is degenerated. Closely related forms of the protein, composed of the same number of domains (six), are found in all Gram-negative bacteria. More distant proteins, generally formed of fewer domains, have been identified, by sequence similarities, in Gram-positive bacteria and are also termed ‘S1 proteins’. However in the absence of functional information, it is generally difficult to ascertain their relationship with Gram-negative S1. In this article, we report the solution structure of the fourth and sixth domains of the E. coli protein S1 and show that it is possible to characterize their β-barrel by a consensus sequence that allows a precise identification of all domains in Gram-negative and Gram-positive S1 proteins. In addition, we show that it is possible to discriminate between five domain types corresponding to the domains 1, 2, 3, 4–5 and 6 of E. coli S1 on the basis of their sequence. This enabled us to identify the nature of the domains present in Gram-positive proteins and, subsequently, to probe the filiations between all forms of S1.


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