Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA

Proteins of the RsmA/ CsrA family are global translational regulators in many bacterial species. We have determined the solution structure of a complex formed between the RsmE protein, a member of this family from Pseudomonas fluorescens, and a target RNA encompassing the ribosome- binding site of the hcnA gene. The RsmE homodimer with its two RNA- binding sites makes optimal contact with an 5'-(A)/(U)CANGGANGU/A-(3)' sequence in the mRNA. When tightly gripped by RsmE, the ANGGAN core folds into a loop, favoring the formation of a 3- base- pair stem by flanking nucleotides. We validated these findings by in vivo and in vitro mutational analyses. The structure of the complex explains well how, by sequestering the Shine- Dalgarno sequence, the RsmA/ CsrA proteins repress translation.