Structural approaches for the DNA binding motifs prediction in Bacillus thuringiensis sigma-E transcription factor (σTF).

The sigma-E transcription factor (σTF) can be found in most of the bacteria cells including Bacillus thuringiensis. However, the cellular regulatory mechanisms of these transcription factors in the mass production of δ-endotoxins during sporulation stage are yet to be revealed. In addition, the recognition of DNA towards σTF DNA binding motifs that led to the transcription activities is also being poorly studied. Therefore, this work studied the possible DNA binding motifs of σTF by utilising in silico approaches. The structure of σTF was first built via three different computational methods. A cognate DNA sequence was then docked to the predicted σTF DNA-binding motifs. The binding free energy calculated using molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) for triplicate 50 ns simulation of σTF-DNA complex revealed favourable binding energy of DNA to σTF (average ∆G = -34.57 kcal/mol) mainly driven by non-polar interactions. This study revealed that σTF LYS131, ARG133, PHE138, TRP146, ARG222, LYS225 and ARG226 are most likely the key residues upon the binding and recognition of DNA prior to transcription actives. Since determination of genome-regulating protein which recognises specific DNA sequence is important to discriminate between the proteins preferences for different genes, this study might provide some understanding on the possible σTF-DNA recognition prior to transcription initiated for the δ-endotoxins production.