The poly(A) binding protein Hfq protects RNA from RNase E and exoribonucleolytic degradation.
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.
Folichon
Marc
M
UPR CNRS No. 9073, Conventionnée avec l'Université Paris 7-Denis Diderot, Institut de Biologie Physico-Chimique, 75005 Paris, France.
Arluison
Véronique
V
Pellegrini
Olivier
O
Huntzinger
Eric
E
Régnier
Philippe
P
Hajnsdorf
Eliane
E
D001483:Base Sequence; D001665:Binding Sites; D024202:Electrophoretic Mobility Shift Assay; D004722:Endoribonucleases / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D005095:Exoribonucleases / Q000378:metabolism; D035001:Host Factor 1 Protein / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011061:Poly A / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011117:Polyribonucleotide Nucleotidyltransferase / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000235:genetics; D013379:Substrate Specificity; D013816:Thermodynamics
D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D012333:RNA, Messenger; D012269:Ribosomal Proteins; C036004:ribosomal protein S15; D011061:Poly A; D011117:Polyribonucleotide Nucleotidyltransferase; D004722:Endoribonucleases; D005095:Exoribonucleases; C022535:exoribonuclease II; C022537:ribonuclease E