Figure 3.

TPP riboswitch in transcription termination of B.subtilis. (A) The depicted secondary structure of the wild type according to the riboswitch model (3) possesses a stable terminator hairpin, downstream of the evolutionary conserved bases in the thi-box. The anti-antiterminator structure (3) that prohibits the emergence of an antiterminator structure as in (B), guarding the terminator hairpin in the presence of TPP, is located upstream of the terminator. (B) Mutated riboswitch; predicted mutation A158U with respect to the wild-type structure in (A) leads to the emergence of the same antiterminator structure as in the absence of TPP. An antiterminator structure is challenging to obtain as a consequence of introducing a single point mutation. It is possible to efficiently locate this predicted peculiar mutation using the eigenvalue method described in the text, after generating Table 1 and noticing the eigenvalue λ₂ = 0.223239. All other single point mutations that have been computationally tried will retain the stable terminator hairpin.