Mechanism for a transcriptional activator that works at the isomerization step

Abstract

Transcriptional activators in prokaryotes have been shown to stimulate different steps in the initiation process including the initial binding of RNA polymerase (RNAP) to the promoter and a postbinding step known as the isomerization step. Evidence suggests that activators that affect initial binding can work by a cooperative binding mechanism by making energetically favorable contacts with RNAP, but the mechanism by which activators affect the isomerization step is unclear. A well-studied example of an activator that normally exerts its effect exclusively on the isomerization step is the bacteriophage lambda cl protein (lambda cl), which has been shown genetically to interact with the C-terminal region of the sigma (70) subunit of RNAP, We show here that the interaction between hcl and sigma can stimulate transcription even when the relevant portion of sigma is transplanted to another subunit of RNAP, This activation depends on the ability of Acl to stabilize the binding of the transplanted sigma moiety to an ectopic -35 element. Based on these and previous findings, we discuss a simple model that explains how an activator's ability to stabilize the binding of an RNAP subdomain to the DNA can account for its effect on either the initial binding of RNAP to a promoter or the isomerization step.