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Expression of the  trpEDCFBA  operon of  Bacillus subtilis  is regulated by transcription attenuation and translation control mechanisms. We recently determined that the  B. subtilis trp  leader readthrough transcript can adopt a Mg 2+ -dependent tertiary structure that appears to interfere with TRAP-mediated translation control of  trpE . In the present study, sequence comparisons to  trp  leaders from three other  Bacillus  sp. were made, suggesting that RNA secondary and tertiary structures are phylogenetically conserved. To test this hypothesis, experiments were carried out with the  trp  leader transcript from  Bacillus stearothermophilus . Structure mapping experiments confirmed the predicted secondary structure. Native gel experiments identified a faster mobility species in the presence of Mg 2+ , suggesting that a Mg 2+ -dependent tertiary structure forms. Mg 2+ -dependent protection of residues within the first five triplet repeats of the TRAP binding target and a pyrimidine-rich internal loop were observed, consistent with tertiary structure formation between these regions. Structure mapping in the presence of a competitor DNA oligonucleotide allowed the interacting partners to be identified as a single-stranded portion of the purine-rich TRAP binding target and the large downstream pyrimidine-rich internal loop. Thermal denaturation experiments revealed a Mg 2+ - and pH-dependent unfolding transition that was absent for a transcript missing the first five triplet repeats. The stability of several mutant transcripts allowed a large portion of the base-pairing register for the tertiary interaction to be determined. These data indicate that RNA secondary and tertiary structures involved in TRAP-mediated translation control are conserved in at least four  Bacillus  species.

Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus