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Nucleic Acids Research Advance Access originally published online on February 17, 2009
Nucleic Acids Research 2009 37(7):2126-2141; doi:10.1093/nar/gkp078
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Nucleic Acids Research, 2009, Vol. 37, No. 7 2126-2141
© 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.

RNA

A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins

Akiko Takeuchi1, David Schmitt1, Charles Chapple2, Elena Babaylova1,3, Galina Karpova3, Roderic Guigo2, Alain Krol1,* and Christine Allmang1

1Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 Rue René Descartes, 67084 Strasbourg, France, 2Centre de Regulacio Genomica, Genome Bioinformatics Research Group, Parc de Recerca Biomedica de Barcelona, c/Dr. Aiguader 88, 08003 Barcelona, Spain and 3Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentjeva 8, Novosibirsk, 630090, Russia

*To whom correspondence should be addressed. Tel: +33 3 88 41 70 50; Fax: +33 3 88 60 22 18; Email: a.krol{at}ibmc.u-strasbg.fr

Received December 17, 2008. Revised January 27, 2009. Accepted January 27, 2009.

Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3'UTR of selenoprotein mRNAs, and trans-acting factors. Among these, the SECIS Binding Protein 2 (SBP2) is central to the mechanism. SBP2 has been so far functionally characterized only in rats and humans. In this work, we report the characterization of the Drosophila melanogaster SBP2 (dSBP2). Despite its shorter length, it retained the same selenoprotein synthesis-promoting capabilities as the mammalian counterpart. However, a major difference resides in the SECIS recognition pattern: while human SBP2 (hSBP2) binds the distinct form 1 and 2 SECIS RNAs with similar affinities, dSBP2 exhibits high affinity toward form 2 only. In addition, we report the identification of a K (lysine)-rich domain in all SBP2s, essential for SECIS and 60S ribosomal subunit binding, differing from the well-characterized L7Ae RNA-binding domain. Swapping only five amino acids between dSBP2 and hSBP2 in the K-rich domain conferred reversed SECIS-binding properties to the proteins, thus unveiling an important sequence for form 1 binding.

Present address: David Schmitt, Novartis, Basel, Switzerland.


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