Bioinformatics analysis of extracellular subtilisin E from Bacillus subtilis

Abstract

Bacillus spp. are the main sources of subtilisin E, which has several applications in biotechnology. The 3D structure of subtilisin E has a significant impact on its efficacy. In this study, we evaluated subtilisin E from Bacillus subtilis subsp. subtilis str. 168 by bioinformatic methods. The results revealed that the subtilisin E sequence from B. subtilis contains highly conserved amino acids, including histidine (H), aspartic acid (D) and serine (S). Subtilisin E cleaves the bonds between hydrophobic and polar amino acids in keratin-associated proteins. The effects of point mutations on the crystal structure of subtilisin E (PDB ID: 1SCJ) showed that changes of asparagine 123 (N123) to valine (V) and serine 331 (S331) to leucine (L) respectively, were the most stabilizing. Genomic analysis of the subtilisin E-coding gene (aprE) indicated that this gene and the yhfN gene are expressed through a σA promoter. The analysis of TBFs revealed AbrB, ScoC, DegU, Hpr, σA, SinR, TenA, and DegU as relevant regulators of aprE expression. Phylogenetic analysis showed that subtilisin Es have highly conserved structures among Bacillus spp., sharing a common ancestor, where their coding genes were duplicated and evolved within the Bacillus spp. As the conclusion, our in silico study demonstrated that the overexpression of the aprE gene and stability of the produced subtilisin E can be improved though system biology methods such as point mutations and identifying the involved transcription factors (TFs) or/and TBFs.

Communicated by Ramaswamy H. Sarma

Keywords:

• Subtilisin E
• keratinase
• alkaline serine protease
• Bacillus subtilis
• bioinformatics

Acknowledgements

To perform this study, RZE and BY received a research grant from the National Institute of Genetic Engineering and Biotechnology (NIGEB) of Islamic Republic of Iran. We would like to thank Dr. Parvin Shariati (NIGEB, Tehran, Iran) for the English editing of the manuscript.

Disclosure statement

The authors declare that they have no conflict of interests.

Additional information

Funding

To perform this study, RZE received a research grant support from the National Institute of Genetic Engineering and Biotechnology (NIGEB) of the Islamic Republic of Iran.