Fig. 5: Activity of C. beijerinckii pfl ZTP riboswitch intact pseudoknot and terminator variants.

a Sequence of the C. beijerinckii pfl ZTP riboswitch consensus variant library annotated to show all pseudoknot and terminator configurations in which variable nucleotides form Watson–Crick base pairs. b Plots showing fraction terminator readthrough for the four variant classes in which variable nucleotides in the pseudoknot and terminator form Watson–Crick base pairs. Variants are plotted along the x-axis by the difference in fraction terminator readthrough measured for the 1 mM ZMP and 0 mM ZMP conditions so that each variant is located at the same x-axis position in both plots. c, d Plots showing the efficiency of each terminator from panel a in the presence of each J1-2 sequence for U113, C116, and ΔU113, ΔC116 variants in the presence of 500 μM NTPs (c) and 100 μM NTPs (d). The median fraction terminator readthrough for each variant group was calculated using the n = 288 variants that comprise the group. e Illustration of an alternative pseudoknot that is favored if J1-2 contains G24. f Illustration of a model for how the identity of the 89:117 terminator base pair affects the propagation of terminator base pairs through the alternative pseudoknot depicted in panel e. Data are from the experiments shown in Figs. 3, 4. Source data are provided as a Source Data file. WT wild type, FL flip, ST strong, WK weak, PK pseudoknot, term terminator, alt. PK alternative pseudoknot.