Structural basis for RNA 3′-end recognition by Hfq
Open Access
- 7 July 2011
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 108 (32), 13065-13070
- https://doi.org/10.1073/pnas.1103420108
Abstract
The homohexameric (L)Sm protein Hfq is a central mediator of small RNA-based gene regulation in bacteria. Hfq recognizes small regulatory RNAs (sRNAs) specifically, despite their structural diversity. This specificity could not be explained by previously described RNA-binding modes of Hfq. Here we present a distinct and preferred mode of Hfq–RNA interaction that involves the direct recognition of a uridine-rich RNA 3′ end. This feature is common in bacterial RNA transcripts as a consequence of Rho-independent transcription termination and hence likely contributes significantly to the general recognition of sRNAs by Hfq. Isothermal titration calorimetry shows nanomolar affinity between Salmonella typhimurium Hfq and a hexauridine substrate. We determined a crystal structure of the complex that reveals a constricted RNA backbone conformation in the proximal RNA-binding site of Hfq, allowing for a direct protein contact of the 3′ hydroxyl group. A free 3′ hydroxyl group is crucial for the high-affinity interaction with Hfq also in the context of a full-length sRNA substrate, RybB. The capacity of Hfq to occupy and sequester the RNA 3′ end has important implications for the mechanisms by which Hfq is thought to affect sRNA stability, turnover, and regulation.Keywords
This publication has 32 references indexed in Scilit:
- RNAs actively cycle on the Sm-like protein HfqJournal of Bone and Joint Surgery, 2010
- Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAsNature Structural & Molecular Biology, 2004
- The Sm‐like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coliMolecular Microbiology, 2004
- The poly(A) binding protein Hfq protects RNA from RNase E and exoribonucleolytic degradationNucleic Acids Research, 2003
- Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAsRNA, 2003
- Global analysis of small RNA and mRNA targets of HfqMolecular Microbiology, 2003
- Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like proteinThe EMBO Journal, 2002
- Transcription termination at intrinsic terminators: the role of the RNA hairpin.Proceedings of the National Academy of Sciences of the United States of America, 1995
- Different Mechanisms of Recognition of Bacteriophage Qβ Plus and Minus Strand RNAs by Qβ ReplicaseJournal of Molecular Biology, 1993
- Factor Fraction required for the Synthesis of Bacteriophage Qβ-RNANature, 1968