8 Protein-Protein Interactions as Critical Determinants of Regulated Initiation and Termination of Transcription

Abstract

OVERVIEW
Protein-protein interactions are critical determinants of regulated transcription. In Escherichia coli the initiation factors bind to RNA polymerase, whereas in mammals at least one polymerase-binding protein, RAP30/74 (TFIIF), is part of the multiprotein RNA polymerase II (pol II) initiation complex. Gene-specific regulators regulate transcription by contacting TFIID or other protein components of the promoter-bound initiation complex. Regulated chain elongation also involves RNA polymerase-binding proteins: NusA in E. coli; SII-like proteins and RAP30/74 in eukaryotes. Transcription termination can then be controlled by specific proteins or by ribonucleoprotein complexes like that assembled by the N protein of bacteriophage λ on the surface of RNA polymerase. Many weak protein-protein interactions involved in transcription can be detected by protein affinity chromatography; some of the most interesting ones remain to be identified.

INTRODUCTION
The regulated synthesis of RNA by RNA polymerase is a complex process in which protein-protein interactions have a major role. For example, proteins that interact with RNA polymerase are fundamental constituents of the transcriptional machinery in prokaryotes (see Fig. 1) and eukaryotes. The first such protein to be discovered, σ⁷⁰ (Burgess et al. 1969), enables RNA polymerase to recognize the −10 and −35 regions of canonical promoters in E. coli (Gardella et al. 1989; Siegele et al. 1989). More minor σ factors enable RNA polymerase to recognize alternative promoter sequences. They play key roles in the development of some bacteriophages, in bacterial responses to certain environmental stimuli, and in the sporulation programs of gram-positive bacteria (Helmann and Chamberlin 1988; Gross et...