Abstract
Transcription initiation is a highly regulated step of gene expression. Here, we discuss the series of large conformational changes set in motion by initial specific binding of bacterial RNA polymerase (RNAP) to promoter DNA and their relevance for regulation. Bending and wrapping of the upstream duplex facilitates bending of the downstream duplex into the active site cleft, nucleating opening of 13 bp in the cleft. The rate-determining opening step, driven by binding free energy, forms an unstable open complex, probably with the template strand in the active site. At some promoters, this initial open complex is greatly stabilized by rearrangements of the discriminator region between the −10 element and +1 base of the nontemplate strand and of mobile in-cleft and downstream elements of RNAP. The rate of open complex formation is regulated by effects on the rapidly-reversible steps preceding DNA opening, while open complex lifetime is regulated by effects on the stabilization of the initial open complex. Intrinsic DNA opening-closing appears less regulated. This noncovalent mechanism and its regulation exhibit many analogies to mechanisms of enzyme catalysis.
Highlights
Transcription is the first step of gene expression and is one of the most fundamental processes of life
RNA polymerase (RNAP) are composed of a core enzyme, which carries out RNA synthesis, and a specificity () subunit for recognition of promoter DNA sequence and subsequent events of initiation (Figures 1 and 2)
We summarize evidence for the series of large conformational changes, set in motion by binding of bacterial RNAP to promoter DNA to form the initial closed complex and involving bending and wrapping of upstream DNA, which allow the downstream duplex DNA to be bent into the active site cleft of RNAP to form an advanced closed complex
Summary
Transcription is the first step of gene expression and is one of the most fundamental processes of life. At some (but not all) promoters, subsequent conformational changes in RNAP and the nontemplate strand stabilize this initial open complex (reviewed in [3]). Studies with Escherichia coli RNAP reveal that the early steps of open complex formation, including initial specific binding to the promoter and some or all of the coupled conformational changes that bend. We first discuss the status of the mechanism of forming and stabilizing the open complex between the E. coli 70 RNAP holoenzyme and promoter DNA, including what is known about the key RNAP structural and DNA sequence determinants of the rates and equilibria of the steps of this mechanism. We briefly discuss implications of this mechanism for regulating the rate of open complex formation
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