Figure 1.

A model for PRE-alx regulation by transcriptional pausing [adapted from (14)]. In the absence of transcriptional pausing, PRE-alx forms a translationally inactive structure, whereas when folding is affected by RNAP pausing, the newly synthesized RNA adopts an active structure in which the ribosome-binding site (in red) is exposed for 30 S ribosomal subunit binding. Formation of the active structure involves pausing of RNAP at two sites located at hairpin C (PC) and hairpin D (PD). On pausing of RNAP (shaded in light blue) at PC, the sequence required to complete stem C is sequestered within the transcription elongation complex and thus formation of hairpin C is prevented. Instead, hairpin S (indicated by a purple line) forms. Similarly, pausing at PD inhibits the formation of hairpin D, allowing base pairing between the complementary sequences in hairpins C and D (in blue) and formation of the apical part of hairpin C/D (in green).