Journal
EMBO JOURNAL
Volume 34, Issue 20, Pages 2557-2573Publisher
WILEY
DOI: 10.15252/embj.201591569
Keywords
ChiX; Hfq; MgrR; RyhB
Categories
Funding
- Intramural Research Program of the National Institutes of Health
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development
- National Cancer Institute
- Center for Cancer Research
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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.
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