ArticleNucleic acids research2020
Crystal structure of an Escherichia coli Hfq Core (residues 2-69)-DNA complex reveals multifunctional nucleic acid binding sites.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 35 citations in OpenAlex.
- Profiling large-scale protein occupancy on bacterial genomes using IPOD-HR.Nature protocols · 2026Review
- Dual Role of Small Noncoding RNA and Hfq in Bacterial DNA Compaction: A New Perspective on Nucleoid Architecture.ACS omega · 2026Article
- DNA methylation enhances cooperative disentanglement by the Hfq nucleoid-associated protein.European biophysics journal : EBJ · 2026Article
- Molecular recognition and structural plasticity in amyloid-nucleic acid complexes.Journal of structural biology · 2025Review
- Bacterial Amyloids as Hubs for Nucleic Acid Interactions: Implications and Mechanisms.International journal of molecular sciences · 2025Review
- Review
- Polyphosphate: The "Dark Matter" of Bacterial Chromatin Structure.Molecular microbiology · 2025Review
- Amyloid-like DNA bridging: a new mode of DNA shaping.Nucleic acids research · 2025Article
- Transcriptome-scale analysis uncovers conserved residues in the hydrophobic core of the bacterial RNA chaperone Hfq required for small regulatory RNA stability.Nucleic acids research · 2025Article
- The Amyloid Assembly of the Bacterial Hfq Is Lipid-Driven and Lipid-Specific.International journal of molecular sciences · 2024Article
- Hfq C-terminal region forms a β-rich amyloid-like motif without perturbing the N-terminal Sm-like structure.Communications biology · 2023Article
- Gene knockdown by structure defined single-stem loop small non-coding RNAs with programmable regulatory activities.Synthetic and systems biotechnology · 2023Article
- Translational regulation by Hfq-Crc assemblies emerges from polymorphic ribonucleoprotein folding.The EMBO journal · 2023Article
- Models of Hfq interactions with small non-coding RNA in Gram-negative and Gram-positive bacteria.Frontiers in cellular and infection microbiology · 2023Review
- Dynamic Refolding of OxyS sRNA by the Hfq RNA Chaperone.Journal of molecular biology · 2022Article
- Unraveling Membrane Perturbations Caused by the Bacterial Riboregulator Hfq.International journal of molecular sciences · 2022Article
- Distinct heterochromatin-like domains promote transcriptional memory and silence parasitic genetic elements in bacteria.The EMBO journal · 2022Article
- Identification of small RNAs associated with RNA chaperone Hfq reveals a new stress response regulator inFrontiers in microbiology · 2022Article
- Amyloid-like Hfq interaction with single-stranded DNA: involvement in recombination and replication inQRB discovery · 2022Article
- Polyphosphate drives bacterial heterochromatin formation.Science advances · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Hfq regulates bacterial gene expression post-transcriptionally by binding small RNAs and their target mRNAs, facilitating sRNA-mRNA annealing, typically resulting in translation inhibition and RNA turnover. Hfq is also found in the nucleoid and binds double-stranded (ds) DNA with a slight preference for A-tracts. Here, we present the crystal structure of the Escherichia coli Hfq Core bound to a 30 bp DNA, containing three 6 bp A-tracts. Although previously postulated to bind to the 'distal' face, three statistically disordered double stranded DNA molecules bind across the proximal face of the Hfq hexamer as parallel, straight rods with B-DNA like conformational properties. One DNA duplex spans the diameter of the hexamer and passes over the uridine-binding proximal-face pore, whereas the remaining DNA duplexes interact with the rims and serve as bridges between adjacent hexamers. Binding is sequence-independent with residues N13, R16, R17 and Q41 interacting exclusively with the DNA backbone. Atomic force microscopy data support the sequence-independent nature of the Hfq-DNA interaction and a role for Hfq in DNA compaction and nucleoid architecture. Our structure and nucleic acid-binding studies also provide insight into the mechanism of sequence-independent binding of Hfq to dsRNA stems, a function that is critical for proper riboregulation.
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