Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σ^D and σ^H deciphered...

This study aimed to reveal interactions of the stress response sigma subunits (factors) σ^D and σ^H of RNA polymerase and promoters in Gram-positive bacterium Corynebacterium glutamicum by combining wet-lab obtained data and in silico modeling. Computer modeling-guided point mutagenesis of C. glutamicum σ^H subunit led to the creation of a panel of σ^H variants. Their ability to initiate transcription from naturally occurring hybrid σ^D/σ^H-dependent promoter Pcg0441 and two control canonical promoters (σ^D-dependent PrsdA and σ^H-dependent PuvrD3) was measured and interpreted using molecular dynamics simulations of homology models of all complexes. The results led us to design the artificial hybrid promoter PD₃₅H₁₀ combining the -10 element of the PuvrD3 promoter and the -35 element of the PrsdA promoter. This artificial hybrid promoter PD_35-rsdAH_10-uvrD3 showed almost optimal properties needed for the bio-orthogonal transcription (not interfering with the native biological processes).