7 Quantitative Aspects of the Transcription Cycle in Escherichia coli

Abstract

OVERVIEW
A quantitative analysis of the transcription cycle of E. coli is presented that incorporates both equilibrium and kinetic elements. We consider the various stages of transcription initiation, the properties of the elongation complex, and the relationship of elongation to termination. Thermodynamic descriptions of the transcription cycle can be cast in the form of free energy diagrams. These can be combined with kinetic descriptions based on activation energy barrier diagrams to provide the basis for a quantitative description of regulatory processes at each stage of the cycle.

INTRODUCTION
In E. coli, control over gene expression is exerted primarily at the level of transcription.3 In this chapter, we deal almost exclusively with the events of transcription catalyzed by the DNA-dependent RNA polymerase of E. coli, since we know far more about this polymerase than about any other. However, it is becoming evident that the RNA polymerases of eukaryotes are related to that of E. coli at both the evolutionary (Sweetser et al. 1987) and the functional levels. We expect that within a few years it will be possible to describe the behavior of eukaryotic transcription systems in comparable detail and that many of the general principles described here will apply to eukaryotes as well.

The Transcription Cycle
The transcription cycle, by which we mean the series of phases through which the RNA polymerase passes in directing transcript formation, is presented in schematic form in Figure 1. This cycle is conventionally divided into the phases of initiation, elongation, and termination. Each of...