Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli

Authors

  • Yoshiki Ikeda,

    1. Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan.
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    • Research Fellow of the Japan Society for the Promotion of Science.

    • Yoshiki Ikeda and Mieko Yago contributed equally to this work.

  • Mieko Yagi,

    1. Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan.
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    • Yoshiki Ikeda and Mieko Yago contributed equally to this work.

  • Teppei Morita,

    1. Faculty of Pharmaceutical Sciences, Suzuka University of Medical Sciences, Suzuka, Mie 513-0816, Japan.
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  • Hiroji Aiba

    Corresponding author
    1. Faculty of Pharmaceutical Sciences, Suzuka University of Medical Sciences, Suzuka, Mie 513-0816, Japan.
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E-mail aiba@suzuka-u.ac.jp; Tel. (+81) 59 340 0573; Fax (+81) 59 368 1271.

Summary

An RNA chaperon Hfq along with Hfq-binding sRNAs stably binds to RNase E in Escherichia coli. The role of the Hfq–RNase E interaction is to recruit RNase E to target mRNAs of sRNAs resulting in the rapid degradation of the mRNA–sRNA hybrid. The C-terminal scaffold region of RNase E is responsible for the interaction with Hfq. Here, we demonstrate that the scaffold region can be deleted up to residue 750 without losing the ability to cause the rapid degradation of target mRNAs mediated by Hfq/sRNAs. The truncated RNase E750 can still bind to Hfq although the truncation significantly reduces the Hfq-binding ability. We conclude that the subregion between 711 and 750 is sufficient for the functional interaction with Hfq to support the rapid degradation of ptsG mRNA although additional subregions within the scaffold are also involved in Hfq binding. Deletion of the 702–750 region greatly impairs the ability of RNase E to cause the degradation of ptsG mRNA. In addition, a polypeptide corresponding to the scaffold region binds to Hfq without the help of RNA. Finally, we demonstrate that overexpression of RhlB partially inhibits the Hfq binding to RNase E and the rapid degradation of ptsG mRNA.

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