The function of the σ-factor of Escherichia coli RNA polymerase in template site selection

Summary

Binding of Escherichia coli RNA polymerase to T4 DNA in the absence or presence of σ-factor was studied, using a “competing template” method determining the amounts of RNA polymerase attached to T4 DNA.

RNA polymerase lacking the σ-factor (core enzyme) was found to bind to T4 DNA at a maximum ratio of 22 μg polymerase/μg DNA, suggesting that the amount of core enzyme bound is limited only by space on the template. In the presence of σ-factor, however, polymerase attachment was found to be restricted to a small number of specific template sites. That the σ-factor prevents nonspecific polymerase attachment is also demonstrated by the finding that addition of σ to nonspecifically bound core enzyme stimulates release of the enzyme from the DNA.

The results further indicate that σ is also required for a step in the process of chain initiation, subsequent to polymerase attachment. This σ-dependent reaction may be responsible for the fact that RNA polymerase-DNA complexes formed in presence of σ are more stable (dissociation rate constant ≦0.0005 min^-1) than those formed in the absence of σ-factor (dissociation rate constant 0.04 min^-1).

RNA polymerase saturated with σ-factor is heterogeneous with respect to the maximum number of enzyme molecules binding to T4 DNA. A comparison of these numbers with the numbers of template sites utilized for chain initiation (determined by Bremer, 1970) suggests

• 1) that the polymerase binding measured occurs at the template sites at which RNA polymerase having a long functional lifetime initiates transcription; “early quitter” RNA polymerase, characterized by a very short functional lifetime (Müller and Bremer, 1969), seems to form unstable complexes with the DNA which are apparently detected by other binding assays;

• 2) that the stable polymerase-DNA complexes contain at least two classes of polymerase molecules which seem to bind to the same promoter sites (17/T4 genome) at different multiplicities (1 o4 7 molecules/promoter, respectively).