Figure 7

RNA secondary structure upstream of pvuIIR. A. Putative alternative hairpins in pvuIICR mRNA. The sequence from the pvuIIC gene just upstream of pvuIIR is shown, with numbering corresponding to that in Figure 3A. As previously described [9], the program MFOLD [61] predicts alternative hairpin structures, the downstream one of which would occlude the RBS (structure on right, green highlight). The orange highlighting shows a sequence shared between the two structures, making them mutually exclusive. The red circle indicates the position of a termination product in previous primer extension reactions [7]. The boundaries of two in-frame deletions are indicated. B. Effect of in-frame hairpin arm deletions on translation of pvuIIR. The deletions shown in (A) were introduced into the pvuIIR-lacZ translational fusion, and β-galactosidase activity was measured as described for Figure 4. This was repeated in the presence of WT (closed symbols, gray bars) or null mutant forms of C.PvuII (open symbols, white bars) provided in trans from compatible plasmids. Plot of activity vs. culture density, for WT (circles), arm 1 deletion mutant (squares), or arm 2 deletion mutant (triangles). C. Slopes from (B) are shown to facilitate comparison.