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. 2020 Nov 24;48(21):12336–12347. doi: 10.1093/nar/gkaa1139

Figure 1.

Figure 1.

Model of standby-mediated translation of tisB mRNA involving a pseudoknot. (A) The steps involved in translation of tisB mRNA are detailed in the Introduction. The sequestered tisB RBS (green) and single-stranded standby site (blue) are indicated. Translation requires transient S1-guided 30S subunit binding to the standby site to promote structure unwinding towards the RBS. The functional standby region contains a single stranded region (blue) and a 5′-end structure (red). (B) Schematics of an H-type RNA pseudoknot showing characteristic stem (S1 and S2) and loop (L1, L2 and L3) features. (C) Secondary structure of the 5′ end region of +42 tisB mRNA with nucleotide sequence information. The unstructured standby site is in blue. Dashed lines indicate base-pairing that would generate a pseudoknot via formation of a second stem, S2 (grey box: left flank of stem; black box: right flank). (D) Pseudoknot model schematic for the 5′ end segment of +42 tisB mRNA, based on HotKnots software predictions (see Results). General features: S1 = 9 nt, S2 = 5 nt, L1 = 0 nt, L2 = 2 nt and L3 = 3 nt) (E) Point mutations used in this work. Color code as in C.