FIG 7.

Cdi2_4 riboswitch transcription regulation requires specific c-di-GMP binding. (A) Predicted secondary structure and tertiary interactions of the Cdi2_4 aptamer upstream of pilA1. The cdi2_4 aptamer structure is based on the three-dimensional structure of the Cac-1-2 c-di-GMP-II aptamer from Clostridium acetobutylicum (64). For clarity, P1 (blue), P2 (gray), P3 (purple), and P4/pseudoknot (green) are shown in color. The c-di-GMP molecule is shown in red. Positions 69, 70, and 73 correspond to nucleotides interacting with c-di-GMP in Cac-1-2. Bases pairs are indicated with standard symbols (89). (B) Single-round in vitro transcription of the Cdi2-4 riboswitch. Transcription reactions were performed on DNA templates carrying no mutation (WT) or a single-nucleotide substitution (A70C and A70G) without or with 10 μM c-di-GMP or c-di-AMP. Read-through (RT) and terminated (T) products are indicated on the right. The percentages of read-through (RT %) products are indicated under every lane.