In silico Analysis and Molecular Modeling of RNA Polymerase, Sigma S (RpoS) Protein in Pseudomonas aeruginosa PAO1

• Main Authors: Mansour Sedighi, Mohsen Moghoofei, Ebrahim Kouhsari, Abazar Pournajaf, Behzad Emadi, Masoud Tohidfar, Mehrdad Gholami
• Format: Article
• Language: English
• Published: Varastegan Institute for Medical Sciences 2015-10-01
• Series: Reports of Biochemistry and Molecular Biology
• Subjects: Bioinformatics; In silico; Pseudomonas aeruginosa; RpoS; Therapy
• Online Access: http://rbmb.net/article-1-69-en.pdf

Background: Sigma factors are proteins that regulate transcription in bacteria. Sigma factors can be activated in response to different environmental conditions. The rpoS (RNA polymerase, sigma S) gene encodes sigma-38 (σ38, or RpoS), a 37.8 kDa protein in Pseudomonas aeruginosa (P. aeruginosa) strains. RpoS is a central regulator of the general stress response and operates in both retroactive and proactive manners; not only does it allow the cell to survive environmental challenges; it also prepares the cell for subsequent stresses (cross-protection). Methods: The significance of RpoS for stress resistance and protein expression in stationary-phase P. aeruginosa cells was assessed. The goal of the current study was to characterize RpoS of P. aeruginosa PAO1 using bioinformatics tools. Results: The results showed that RpoS is an unstable protein that belongs to the sigma-70 factor family. Secondary structure analysis predicted that random coil is the predominant structure followed by extended alpha helix. The three-dimensional (3D) structure was modeled using SWISS-MODEL Workspace. Conclusion: Determination of sequence, function, structure, and predicted epitopes of RpoS is important for modeling of inhibitors that will help in the design of new drugs to combat multi-drug-resistant (MDR) strains. Such information may aid in the development of new diagnostic tools, drugs, and vaccines for treatment in endemic regions.