The σ54-RNA polymerase holoenzyme binds to promoters that have the two consensus sequences. However, unlike other RNA polymerase holoenzymes, it cannot activate transcription without assistance of an activator protein. The activation process, which is shown schematically, begins with the binding of activator protein to a site on the bacterial chromosome called an enhancer. which is usually 100 bp or more upstream from the σ54 promoter. Interaction between the activator proteins and σ54-holoenzyme is possible because the DNA segment between the two protein-binding sites bends to form a loop.
Although the nucleotide sequence between the two protein binding sites may produce DNA bending, an additional protein such as the integration host factor (IHF) is sometimes required to assist the bending. Activator proteins are themselves subject to regulation by the binding of a small effector molecule or, more commonly, by the addition of a phosphate group to a specific site on the activator protein. Activation induces an ATPase activity within the activator protein that is essential for unwinding DNA in the promoter region so that transcription can begin.
