A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillus subtilis: RNA structure rather than sequence provides interaction specificity.

The Gram-positive soil bacterium Bacillus subtilis transports glucose by the phosphotransferase system. The genes for this system are encoded in the ptsGHI operon. The expression of this operon is controlled at the level of transcript elongation by a protein-dependent riboswitch. In the absence of glucose a transcriptional terminator prevents elongation into the structural genes. In the presence of glucose, the GlcT protein is activated and binds and stabilizes an alternative RNA structure that overlaps the terminator and prevents termination. In this work, we have studied the structural and sequence requirements for the two mutually exclusive RNA structures, the terminator and the RNA antiterminator (the RAT sequence). In both cases, the structure seems to be more important than the actual sequence. The number of paired and unpaired bases in the RAT sequence is essential for recognition by the antiterminator protein GlcT. In contrast, mutations of individual bases are well tolerated as long as the general structure of the RAT is not impaired. The introduction of one additional base in the RAT changed its structure and resulted in complete loss of interaction with GlcT. In contrast, this mutant RAT was efficiently recognized by a different B.subtilis antitermination protein, LicT.