Protein-protein communication within the transcription apparatus

Despite the rapid expansion of catalogues of cis-acting transcription signals on DNA and of trans-acting transcription regulatory proteins found in both prokaryotes and eukaryotes, relatively little is known about precisely how these transcription signals and factors ultimately influence transcription. Recent progress in studies of the molecular anatomy of Escherichia coli RNA polymerase, however, has led to a breakthrough in our understanding of the molecular mechanisms underlying transcription regulation by transcription factors. The RNA polymerase holoenzyme of E. coli is composed of core enzyme with the subunit structure a2133' and one of the several species of v subunit which are involved in the specific recognition of promoters. The core enzyme is the basic machinery ofRNA synthesis: the catalytic site of RNA polytherization is located on the 1 subunit, while RNA polym rase binds to DNA nonspecifically via the 13' subunit. Subunit a links these two large subunits into the core enzyme complex (for reviews, see references 15, 17, and 43). The core enzyme is functionally differentiated into the various forms of holoenzyme by binding one of the different molecular species of cr subunit (for a review, see reference 10). Simple promoters are recognized by one or more of these holoenzymes, but some promoters require additional transcription factors for transcription initiation (1, 16, 17). An increasing amount of evidence indicates that interplay between RNA polymerase and transcription factors involves direct protein-protein contacts (19). Thus, the molecular architecture of the transcription apparatus for specific and accurate initiation differs in detail from promoter to promoter. Each transcription apparatus is responsible for transcription of only a set of genes. Since the number of core enzyme molecules is fixed at a constant level characteristic of the rate of cell growth, i.e., on average about 2,000 molecules per genome equivalent of DNA, the degree to which each of the approximately 4,000 genes on the E. coli chromosome is transcribed is primarily determined by the relative numbers of each kind of transcription apparatus with a particular promoter selectivity (16, 18). In this article, I will summarize the protein-protein communication between RNA polymerase and transcription factors from E. coli.