Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition

• Published in: The EMBO journal 2015-10, Vol.34 (20), p.2557-2573
• Main Authors: Schu, Daniel J, Zhang, Aixia, Gottesman, Susan, Storz, Gisela
• Format: Article
• Language: English
• Subjects: Bacteria; Base Pairing; beta-Galactosidase; Blotting, Northern; ChiX; DNA Primers - genetics; EMBO23; EMBO36; Escherichia coli K12 - genetics; Escherichia coli K12 - metabolism; Escherichia coli Proteins - metabolism; Hfq; Host Factor 1 Protein - metabolism; MgrR; Models, Molecular; Molecular biology; Plasmids - genetics; Protein Binding; Ribonucleic acid; RNA; RNA, Messenger - metabolism; RNA, Small Untranslated - metabolism; RyhB
• ISSN: 0261-4189; 1460-2075
• DOI: 10.15252/embj.201591569

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. Synopsis The RNA chaperone Hfq is required for most sRNA‐mediated regulation in bacteria. This study finds that sRNAs and mRNAs utilize distinct binding surfaces on Hfq, resulting in a combinatorial interaction that determines both sRNA stability and regulatory strength. Hfq‐binding sRNAs and their target mRNAs fall into two classes, reflecting different modes of binding to Hfq. Class I sRNAs bind the proximal and rim surfaces of Hfq, while their mRNA targets bind the distal surface. Class II sRNAs bind the proximal and distal surfaces of Hfq, while their mRNA targets bind the rim. Class II sRNAs are generally more stable and may exclude class I mRNAs from binding Hfq. Graphical Abstract The RNA chaperone Hfq is required for most sRNA‐mediated regulation in bacteria. This study finds that sRNAs and mRNAs utilize distinct binding surfaces on Hfq, resulting in a combinatorial interaction that determines both sRNA stability and regulatory strength.