title: In silico analysis and molecular modeling of RNA polymerase, sigma S (RpoS) protein in Pseudomonas aeruginosa PAO1.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
authors.forename: Mansour
authors.initials: M
authors.lastname: Sedighi
authors.affiliation: Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
authors.forename: Mohsen
authors.initials: M
authors.lastname: Moghoofei
authors.affiliation: Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
authors.forename: Ebrahim
authors.initials: E
authors.lastname: Kouhsari
authors.affiliation: Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
authors.forename: Abazar
authors.initials: A
authors.lastname: Pournajaf
authors.affiliation: Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
authors.forename: Behzad
authors.initials: B
authors.lastname: Emadi
authors.affiliation: Agricultural Biotechnology Research Institute of Iran, Tehran, Iran.
authors.forename: Masoud
authors.initials: M
authors.lastname: Tohidfar
authors.affiliation: Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
authors.forename: Mehrdad
authors.initials: M
authors.lastname: Gholami
keywords: Bioinformatics; In silico; Pseudomonas aeruginosa; RpoS; Therapy