Alternative Hfq‐ sRNA interaction modes dictate alternative mRNA recognition

Abstract

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