Figure 3.

The Imperfectly Complementary “Seed Region” of MicC Is Sufficient to Induce RNase E Mediated Cleavage of ompD.

Denaturing gel showing products of ompD degradation by RNase E (1-762)/RhlB with or without Hfq (lanes 3 and 7) and in the presence of WT MicC with different state of 5′ end (lanes 4-6 in presence of Hfq and 8-10 in absence of Hfq), as well as 12 nucleotides seed region of MicC (lanes 11-12). The RNA chaperone Hfq protects the sRNA and enhances cleavage at the A+83 site. Size markers are in lane 1, control reaction without enzyme is in lane 2. (See also Figures S6, S7, and S8.) The gel was stained with SYBR gold Nucleic Acid Gel Stain, which reveals all the RNA species. The lower band of MicC is a sRNA with 1 nt shorter polyU tail due to different transcription termination by T7 polymerase on polyT stretches.