The stress sigma factor of RNA polymerase RpoS/σ S is a solvent-exposed open molecule in solution

Paola Cavaliere (1) , Sebastien Brier (2, 3) , Petr Filipenko (4) , Christina Sizun (5) , Bertrand Raynal (6) , Françoise Bonneté (7, 8) , Fabienne Levi-Acobas (9) , Jacques Bellalou (9) , Patrick England (6) , Julia Chamot-Rooke (2) , Claudine Mayer (10) , Françoise Norel (1, 11)

1 Systèmes macromoléculaires et Signalisation
2 Spectrométrie de Masse structurale et protéomique
3 UTechS MSBio - Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology
4 Department of Computer Science [New York]
5 ICSN - Institut de Chimie des Substances Naturelles
6 Biophysique Moléculaire (Plate-forme)
7 IBMM - Institut des Biomolécules Max Mousseron [Pôle Chimie Balard]
8 AU - Avignon Université
9 PRPF - Production de Protéines Recombinantes (Plate-Forme)
10 Microb. Struc. (UMR_3528 / U-Pasteur_5) - Microbiologie structurale - Structural Microbiology
11 Biochimie des Interactions Macromoléculaires / Biochemistry of Macromolecular Interactions

In bacteria, one primary and multiple alternative sigma (σ) factors associate with the RNA polymerase core enzyme (E) to form holoenzymes (Eσ) with different promoter recognition specificities. The alternative σ factor RpoS/σ S is produced in stationary phase and under stress conditions and reprograms global gene expression to promote bacterial survival. To date, the three-dimensional structure of a full-length free σ factor remains elusive. The current model suggests that extensive interdomain contacts in a free σ factor result in a compact conformation that masks the DNA-binding determinants of σ, explaining why a free σ factor does not bind double-stranded promoter DNA efficiently. Here, we explored the solution conformation of σ S using amide hydrogen/deuterium exchange coupled with mass spectrometry, NMR, analytical ultracentrifugation and molecular dynamics. Our data strongly argue against a compact conformation of free σ S. Instead, we show that σ S adopts an open conformation in solution in which the folded σ 2 and σ 4 domains are interspersed by domains with a high degree of disorder. These findings suggest that E binding induces major changes in both the folding and domain arrangement of σ S and provide insights into the possible mechanisms of regulation of σ S activity by its chaperone Crl.

Mots clés: RNA polymerase; RpoS; Salmonella; protein conformation; protein structure; sigma factor

Domaines: Sciences du Vivant [q-bio]

Paola Cavaliere, Sebastien Brier, Petr Filipenko, Christina Sizun, Bertrand Raynal, et al.. The stress sigma factor of RNA polymerase RpoS/σ S is a solvent-exposed open molecule in solution. Biochemical Journal, 2018, 475 (1), pp.341 - 354. ⟨10.1042/BCJ20170768⟩. ⟨pasteur-01685123⟩