Figure 5.

The SnoaL_2 domain modulates σ^J activity. (A) A schematic representation of the β-galactosidase assay to evaluate σ^J activity. The target plasmid contained a sigI-promoter fused to a lacZ gene cloned in the pJEM13 vector (56). The donor plasmid contained either σ^J or σ^JΔSnoaL_2 cloned in the pBAD33m vector. The pBAD33m vector served as a control in this experiment. (B) β-galactosidase activity was significantly reduced upon deleting the SnoaL_2 domain (σ^JΔSnoaL_2) when compared to the full-length σ factor. The SnoaL_2 domain is thus unlikely to play the role of a σ factor antagonist (anti-σ factor). (C and D) A mechanistic model for σ^J activity. The influence of the Snoal_2 domain on DNA binding and transcription initiation suggests that the C-terminal domain is an essential part of σ^J (C). The SnoaL_2 domain tethers σ^J₂ and σ^J₄ in an orientation compatible with promoter DNA binding and potentially influences σ^J–RNAP interaction (16). These interactions could be modulated by the binding of small molecules to the SnoaL_2 domain (D). The SnoaL_2 domain can thus modulate σ^J activity by inducing conformational changes that regulate promoter DNA or RNAP binding.