ArticleProceedings of the National Academy of Sciences of the United States of America2011
Structural basis for RNA 3'-end recognition by Hfq.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers.
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Who cites it
135 citing papers in PubMed.
- OmrA sRNA inhibits translation of phosphoenolpyruvate carboxylase to impair TCA-cycle flux.Nucleic acids research · 2026Article
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- Modular small RNA drives the emergence of virulence traits and environmental trade-offs in Vibrio cholerae.Nature communications · 2026Article
- RNA-RNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNA-mRNA pairing.Nucleic acids research · 2025Article
- An RNA sponge directs the transition from feast to famine in Caulobacter crescentus.Nature communications · 2025Article
- Adaptive genetics reveals constraints on protein structure/function by evolving E. coli under constant nutrient limitation.BMC biology · 2025Article
- Bacterial Regulatory Circuits are Linked and Extended by Small RNAs.Journal of molecular biology · 2025Review
- RNA recognition by minimal ProQ fromRNA (New York, N.Y.) · 2025Article
- Two temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA ompX.Nucleic acids research · 2025Article
- Control of iron acquisition by multiple small RNAs unravels a new role for transcriptional terminator loops in gene regulation.Nucleic acids research · 2024Article
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- An acetyltranferase moonlights as a regulator of the RNA binding repertoire of the RNA chaperone Hfq inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- FinO/ProQ-family proteins: an evolutionary perspective.Bioscience reports · 2023Review
- Models of Hfq interactions with small non-coding RNA in Gram-negative and Gram-positive bacteria.Frontiers in cellular and infection microbiology · 2023Review
- Article
- Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- An overview of gene regulation in bacteria by small RNAs derived from mRNA 3' ends.FEMS microbiology reviews · 2022Review
- Unraveling Membrane Perturbations Caused by the Bacterial Riboregulator Hfq.International journal of molecular sciences · 2022Article
- PhoP induces RyjB expression under acid stress in Escherichia coli.Journal of biochemistry · 2022Article
75 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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