A three-way junction and constituent stem-loops as the stimulator for programmed −1 frameshifting in bacterial insertion sequence IS911

Abstract Several signals are required for the programmed frameshifting in translation of IS 911 mRNA. These include a Shine Dalgarno (SD)-like sequence, a slippery sequence of six adenine residues and a guanine residue (A6G) and a 3′ secondary structure. The structure of the mRNA containing these elements was investigated using chemical and enzymatic probing. The probing data show that the 3′ structure is a three-way junction of stems. The function of the three-way junction was investigated by mutagenesis. Disrupting the stability of the structure greatly affects frameshifting and transposition levels as tested by separate in vivo assays. Structural probing and thermal melting profiles indicate that the disrupted three-way junctions have altered structures.