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

The sigma-E transcription factor (sigma(TF)-T-E) 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 delta-endotoxins during sporulation stage are yet to be revealed. In addition, the recognition of DNA towards sigma(TF)-T-E DNA binding motifs that led to the transcription activities is also being poorly studied. Therefore, this work studied the possible DNA binding motifs of sigma(TF)-T-E by utilising in silico approaches. The structure of sigma(TF)-T-E was first built via three different computational methods. A cognate DNA sequence was then docked to the predicted sigma(TF)-T-E DNA-binding motifs. The binding free energy calculated using molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) for triplicate 50 ns simulation of sigma(TF)-T-E-DNA complex revealed favourable binding energy of DNA to sigma(TF)-T-E (average increment G(bind) = -34.57 kcal/mol) mainly driven by non-polar interactions. This study revealed that sigma(TF)-T-E 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 sigma(TF)-T-E-DNA recognition prior to transcription initiated for the delta-endotoxins production.