Fig. 3
Selection and characterization of glycine-ON and -OFF switches from mutant libraries. a ON/OFF ratio of relative fluorescence intensity in the wild-type glycine riboswitch and the selected glycine-ON riboswitches in M9 medium with or without 80 mM glycine in 96-deep-well plates. b ON/OFF ratio of relative fluorescence intensity in the wild-type glycine riboswitch and the selected glycine-OFF riboswitches in M9 with or without  80 mM glycine in 96-deep-well plates. The yellow column indicates the control strain. c GFP/OD600 ratio of MG1655-BSTG, G1655-BS-ON14, and MG1655-BS-OFF6. Strains were cultured in M9 medium supplemented with 0, 7, 13, 27, 80, and 107 mM glycine. All the data are the average values of three independent experiments. d Secondary structure of the wild-type B. subtilis glycine riboswitch. e Mutations in the glycine-OFF riboswitch glyOFF6 affecting the secondary structure. f Mutations in the glycine-ON riboswitch glyON14 affecting the secondary structure. Base-pairing stems were labeled as the P0/kink-turn motif, P1, P2, and P3 with subsections labeled ‘a’ and ‘b’, and junction structures were labeled J1, J2 and JD with subsections labeled ‘*’. Mutant sites were highlighted in green nucleotides and green boxes with mutation information, red shading highlights nucleotides that base pair to form the transcription terminator stem when the riboswitch is in the ‘OFF’ conformation. Riboswitches’ structures and its mutations were analyzed by RNAflod and VARNA 3–93