Abstract
The bacterial Sm-like protein Hfq facilitates RNA-RNA interactions involved in post-transcriptional regulation of the stress response. Specifically, Hfq helps pair noncoding RNAs (ncRNAs) with complementary regions of target mRNAs. To probe the mechanism of this pairing, we generated a series of Hfq mutants and measured their affinity for RNAs like those with which Hfq must associate in vivo. We tested the mutants' DsrA-dependent activation of rpoS, and their ability to stabilize DsrA ncRNA against degradation in vivo. Our results suggest that Hfq has two independent RNA-binding surfaces. In addition to a well-known site around the core of the Hfq hexamer, we observe interactions with the distal face of Hfq, a new locus with which mRNAs and poly(A) sequences associate. Our model explains how Hfq can simultaneously bind a ncRNA and its mRNA target to facilitate the strand displacement reaction required for Hfq-dependent translational regulation.
Publication types
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Research Support, U.S. Gov't, Non-P.H.S.
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Research Support, U.S. Gov't, P.H.S.
MeSH terms
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Amino Acid Sequence
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Bacterial Outer Membrane Proteins / metabolism*
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Bacterial Proteins / metabolism*
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Binding, Competitive
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Calorimetry
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Escherichia coli / chemistry*
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Escherichia coli / genetics
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Escherichia coli / metabolism*
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Escherichia coli Proteins / chemistry*
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Escherichia coli Proteins / genetics
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Escherichia coli Proteins / metabolism*
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Host Factor 1 Protein / chemistry*
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Host Factor 1 Protein / genetics
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Host Factor 1 Protein / metabolism*
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Models, Molecular
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Molecular Sequence Data
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Mutation / genetics
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Poly A / chemistry
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Poly A / metabolism*
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Protein Denaturation
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Protein Structure, Tertiary
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RNA, Messenger / genetics
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RNA, Messenger / metabolism
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RNA-Binding Proteins / chemistry
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RNA-Binding Proteins / genetics
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RNA-Binding Proteins / metabolism
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Sequence Alignment
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Sigma Factor / metabolism*
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Titrimetry
Substances
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Bacterial Outer Membrane Proteins
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Bacterial Proteins
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DrsA protein, E coli
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Escherichia coli Proteins
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Hfq protein, E coli
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Host Factor 1 Protein
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RNA, Messenger
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RNA-Binding Proteins
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Sigma Factor
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sigma factor KatF protein, Bacteria
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Poly A