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EMBO J. 2015 Oct 14;34(20):2557-73. doi: 10.15252/embj.201591569. Epub 2015 Sep 15.

Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition.

Author information

1
Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, USA.
2
Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA.
3
Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, USA gottesms@helix.nih.gov storzg@mail.nih.gov.
4
Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA gottesms@helix.nih.gov storzg@mail.nih.gov.

Abstract

Many bacteria use small RNAs (sRNAs) and the RNA chaperone Hfq to regulate mRNA stability and translation. Hfq, a ring-shaped homohexamer, has multiple faces that can bind both sRNAs and their mRNA targets. We find that Hfq has at least two distinct ways in which it interacts with sRNAs; these different binding properties have strong effects on the stability of the sRNA in vivo and the sequence requirements of regulated mRNAs. Class I sRNAs depend on proximal and rim Hfq sites for stability and turn over rapidly. Class II sRNAs are more stable and depend on the proximal and distal Hfq sites for stabilization. Using deletions and chimeras, we find that while Class I sRNAs regulate mRNA targets with previously defined ARN repeats, Class II sRNAs regulate mRNAs carrying UA-rich rim-binding sites. We discuss how these different binding modes may correlate with different roles in the cell, with Class I sRNAs acting as emergency responders and Class II sRNAs acting as silencers.

KEYWORDS:

ChiX; Hfq; MgrR; RyhB

PMID:
26373314
PMCID:
PMC4609186
DOI:
10.15252/embj.201591569
[Indexed for MEDLINE]
Free PMC Article

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