DNA Binding Properties of thehfqGene Product ofEscherichia coli

Takada, Ayako; Wachi, Masaaki; Kaidow, Akihiro; Takamura, Makoto; Nagai, Kazuo

doi:10.1006/bbrc.1997.7013

Cited by 38 publications

(35 citation statements)

References 18 publications

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“…We expected that Hfq might be associated with our 30 S subunits and be involved in DsrA ncRNA binding. Hfq specifically binds a 3Ј domain in DsrA (26) and has been shown to interact strongly with DNA sequences (29,30). Western blot analysis using Hfq antisera demonstrates it is not present at detectable levels in our 30 S subunit preparations and therefore is not responsible for the interaction of the molecules with the 30 S subunit in our in vitro assays.…”

Section: Discussionmentioning

confidence: 85%

“…DsrA binds to the protein Hfq (21,26), which is associated with ribosomes in E. coli cells (28). Hfq interacts with a variety of RNA and DNA sequences (29,30). Western blotting analysis using Hfq antisera (the kind gift of Gisela Storz) demonstrated no detectable levels of Hfq in either 30 S ribosomal subunit or 70 S ribosome preparations (data not shown), strongly suggesting that binding of the DsrA to the 30 S subunit resulted from an interaction of the ncRNA with 16 S rRNA or small subunit ribosomal proteins.…”

Section: Resultsmentioning

confidence: 99%

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Interactions of the Non-coding RNA DsrA and RpoS mRNA with the 30 S Ribosomal Subunit

Worhunsky

Godek

Litsch

et al. 2003

Journal of Biological Chemistry

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Section: Discussionmentioning

confidence: 85%

Section: Resultsmentioning

confidence: 99%

Interactions of the Non-coding RNA DsrA and RpoS mRNA with the 30 S Ribosomal Subunit

Worhunsky

Godek

Litsch

et al. 2003

Journal of Biological Chemistry

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“…When nonspecific DNA-binding proteins were analyzed using such DNA fragment mixtures, the longer DNA fragments tend to shift at lower protein concentrations than the shorter fragments (32). The order of DNA binding affinity measured in this system was essentially the same at least among the nonspecific DNA-binding proteins (data not shown).…”

Section: Purificationmentioning

confidence: 89%

Twelve Species of the Nucleoid-associated Protein from Escherichia coli

Azam¹,

Ishihama²

1999

Journal of Biological Chemistry

426

314

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“…E. coli Hfq and its bacterial homologs have been implicated in various facets of bacterial metabolism, including stressinduced sRNA regulation of mRNA translation as well as mRNA stability. In addition to its well-documented interaction with RNA, Hfq has been found associated with DNA (Takada et al 1997;Azam et al 2000;Updegrove et al 2010) as well as a number of proteins (Butland et al 2005). The nature of Hfq's interactions with DNA and many of the proteins are not well understood; however, there is increasing recognition that they may reflect additional functions of Hfq (Le Derout et al 2010).…”

Section: Introductionmentioning

confidence: 99%

The stoichiometry of the Escherichia coli Hfq protein bound to RNA

Updegrove¹,

Correia²,

Chen³

et al. 2011

RNA

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The Escherichia coli RNA binding protein Hfq is involved in many aspects of post-transcriptional gene expression. Tight binding of Hfq to polyadenylate sequences at the 39 end of mRNAs influences exonucleolytic degradation, while Hfq binding to small noncoding RNAs (sRNA) and their targeted mRNAs facilitate their hybridization which in turn effects translation. Hfq binding to an A-rich tract in the 59 leader region of the rpoS mRNA and to the sRNA DsrA have been shown to be important for DsrA enhanced translation initiation of this mRNA. The complexes of Hfq-A 18 and Hfq-DsrA provide models for understanding how Hfq interacts with these two RNA sequence/structure motifs. Different methods have reported different values for the stoichiometry of Hfq-A 18 and Hfq-DsrA. In this work, mass spectrometry and analytical ultracentrifugation provide direct evidence that the strong binding mode of the Hfq hexamer (Hfq 6 ) for A 18 and domain II of DsrA (DsrA DII ) involve 1:1 complexes. This stoichiometry was also supported by fluorescence anisotropy and a competition gel mobility shift experiment using wild-type and truncated Hfq. More limited studies of Hfq binding to DsrA as well as to the sRNAs RprA, OxyS, and an 18-nt segment of OxyS were also consistent with 1:1 stoichiometry. Mass spectrometry of crosslinked samples of Hfq 6 , A 18 , and DsrA DII exhibit intensity corresponding to a ternary 1:1:1 complex; however, the small intensity of this peak and fluorescence anisotropy experiments did not provide evidence that this ternary complex is stable in solution.

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DNA Binding Properties of thehfqGene Product ofEscherichia coli

Cited by 38 publications

References 18 publications

Interactions of the Non-coding RNA DsrA and RpoS mRNA with the 30 S Ribosomal Subunit

Interactions of the Non-coding RNA DsrA and RpoS mRNA with the 30 S Ribosomal Subunit

Twelve Species of the Nucleoid-associated Protein from Escherichia coli

The stoichiometry of the Escherichia coli Hfq protein bound to RNA

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