In silico characterization and comparative analysis of Bacillus subtilis GntR type LutR transcription factor

Abstract

Background: The GntR-type transcriptional factor LutR (formerly YvfI) behaves as a transition stateregulator, governing adaptations of Bacillus subtilis cells to the transition from exponential growthto stationary phase.Material and Methods: In this study, we evaluated a total of 30 LutR proteins from differentbacterial species that were available in the NCBI database. By performing the physicochemicalanalyses, domain analysis, and phylogenetic tree construction, we identified some similarities anddifferences among these 30 LutR proteins. Furthermore, only the primer structure of Bacillus subtilis168 LutR was compared with the sequences and 3D conformational situations of the well-knownHTH-type transcriptional factors FadR (PDB ID: 1HW1, 1HW2, 1HT9) and YvoA (PDB ID: 2WV0) usingPyMOL.Results: These analyses revealed that the critical residues for DNA-recognition and DNA-binding ofLutR are highly conserved and conformationally correspond to the same positions as those in FadRand YvoA. The sequence (15-SVQALAESF-23) of the second helix in LutR seems to be important forDNA-binding, while the Q17-R27-Q47 residues might be critical for DNA recognition. Here, weprovide a detailed description of the similarities and differences between B. subtilis LutR and boththe other LutR proteins from different bacterial species and other HTH-type transcriptional factors.Conclusions: These results provide a scientific groundworkbase and can be used for advanced insilico analysis, homology modelling, and in vitro studies, including DNA-protein interaction analysis,such as ChIP and EMSA methods.