Interactions of the Non-coding RNA DsrA and RpoS mRNA with the 30 S Ribosomal Subunit

Expression of ςs, the gene product of rpoS, is controlled translationally in response to many environmental stresses. DsrA, a small 87-nucleotide non-coding RNA molecule, acts to increase translational efficiency of RpoS mRNA under some growth conditions. In this work, we demonstrate that DsrA binds directly to the 30 S ribosomal subunit with an observed equilibrium affinity of 2.8 × 107m−1. DsrA does not compete with RpoS mRNA or tRNAfMet for binding to the 30 S subunit. The 5′ end of DsrA binds to 30 S subunits with an observed equilibrium association constant of 2.0 × 106m−1, indicating that the full affinity of the interaction requires the entire DsrA sequence. In order to investigate translational efficiency of RpoS mRNA, we examined both ribosome-binding site accessibility and the binding of RpoS mRNA to 30 S ribosomal subunits. We find that that ribosome-binding site accessibility is modulated as a function of divalent cation concentration during mRNA renaturation and by the presence of an antisense sequence that binds to nucleotides 1–16 of the RpoS mRNA fragment. The ribosome-binding site accessibility correlates with the amount of RpoS mRNA participating in 30 S-mRNA “pre-initiation” translational complex formation and provides evidence that regulation follows a competitive model of regulation.