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Nucleic Acids Research, 2003, Vol. 31, No. 24 7302-7310
© 2003 Oxford University Press

Article

The poly(A) binding protein Hfq protects RNA from RNase E and exoribonucleolytic degradation

Marc Folichon, Véronique Arluison, Olivier Pellegrini, Eric Huntzinger1, Philippe Régnier and Eliane Hajnsdorf*

UPR CNRS No. 9073, Conventionnée avec l’Université Paris 7–Denis Diderot, Institut de Biologie Physico-Chimique, 75005 Paris, France and 1 UPR CNRS No. 9002, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France

*To whom correspondence should be addressed. Tel: +33 1 58 41 51 26; Fax: +33 1 58 41 50 20; Email: eliane.hajnsdorf{at}ibpc.fr

The Hfq protein, which shares sequence and structural homology with the Sm and Lsm proteins, binds to various RNAs, primarily recognizing AU-rich single-stranded regions. In this paper, we study the ability of the Escherichia coli Hfq protein to bind to a polyadenylated fragment of rpsO mRNA. Hfq exhibits a high specificity for a 100-nucleotide RNA harboring 18 3'-terminal A-residues. Structural analysis of the adenylated RNA–Hfq complex and gel shift assays revealed the presence of two Hfq binding sites. Hfq binds primarily to the poly(A) tail, and to a lesser extent a U-rich sequence in a single-stranded region located between two hairpin structures. The oligo(A) tail and the interhelical region are sensitive to 3'–5' exoribonucleases and RNase E hydrolysis, respectively, in vivo. In vitro assays demonstrate that Hfq protects poly(A) tails from exonucleolytic degradation by both PNPase and RNase II. In addition, RNase E processing, which occurred close to the U-rich sequence, is impaired by the presence of Hfq. These data suggest that Hfq modulates the sensitivity of RNA to ribonucleases in the cell.


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