RNA Polymerase Holoenzyme Consists of the Core Enzyme and Sigma Factor

KEY CONCEPTS
- Bacterial RNA polymerase can be divided into the α₂ ββ′ω core enzyme that catalyzes transcription and the σ subunit that is required only for initiation.
- Sigma factor changes the DNA-binding properties of RNA polymerase so that its affinity for general DNA is reduced and its affinity for promoters is increased.
The core enzyme has general affinity for DNA, primarily because of electrostatic interactions between the protein, which is basic, and the DNA, which is acidic. When bound to DNA in this fashion, the DNA remains in duplex form. Core enzyme has the ability to synthesize RNA on a DNA template, but it cannot recognize promoters.
The form of the enzyme responsible for initiating transcription from promoters is called the holoenzyme (α₂ ββ′ωσ) (see FIGURE 1). It differs from the core enzyme by containing a sigma factor. Sigma factor not only ensures that bacterial RNA polymerase initiates transcription from specific sites, but it also reduces binding to nonspecific sequences. The association constant for binding of core to DNA is reduced by a factor of ~10⁴ , and the half-life of the complex is less than 1 second, whereas holoenzyme binds to promoters much more tightly, with an association constant ~1,000 times higher on average and a half-life that can be as long as several hours. Thus, sigma factor substantially destabilizes promoter-nonspecific binding.

FIGURE 1. Core enzyme binds indiscriminately to any DNA. Sigma factor reduces the affinity for sequence-independent binding and confers specificity for promoters.
The rate at which the holoenzyme binds to different promoter sequences varies widely, and thus this is an important parameter in determining promoter strength; that is, the efficiency of an individual promoter in initiating transcription. The frequency of initiation varies from about once per second for rRNA genes under optimal conditions to less than one every 30 minutes for some other promoters. Sigma factor is usually released when the RNA chain reaches less than about 10 nucleotides in length, leaving the core enzyme responsible for elongation.