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In many Gram-negative bacteria, including  Salmonella enterica  serovar Typhimurium ( S . Typhimurium), the sigma factor RpoS/σ S  accumulates during stationary phase of growth, and associates with the core RNA polymerase enzyme (E) to promote transcription initiation of genes involved in general stress resistance and starvation survival. Whereas σ factors are usually inactivated upon interaction with anti-σ proteins, σ S  binding to the Crl protein increases σ S  activity by favouring its association to E. Taking advantage of evolution of the σ S  sequence in bacterial species that do not contain a  crl  gene, like  Pseudomonas aeruginosa , we identified and assigned a critical arginine residue in σ S  to the  S . Typhimurium σ S -Crl binding interface. We solved the solution structure of  S.  Typhimurium Crl by NMR and used it for NMR binding assays with σ S  and to generate  in silico  models of the σ S -Crl complex constrained by mutational analysis. The σ S -Crl models suggest that the identified arginine in σ S  interacts with an aspartate of Crl that is required for σ S  binding and is located inside a cavity enclosed by flexible loops, which also contribute to the interface. This study provides the basis for further structural investigation of the σ S -Crl complex.

Binding interface between the Salmonella σS/RpoS subunit of RNA polymerase and Crl: hints from bacterial species lacking crl