Specificity of DNA-protein interactions within transcription complexes of Escherichia coli

The identification of DNA-protein and protein-protein contacts in transcription complexes is a necessary part of the description of each novel promoter. The experimental approaches used for this purpose allow affiliation of the given promoter to the regulon of one of seven alternative 6 subunits of RNA polymerase and determining the dependence of its activity on known protein and nonprotein factors. The nucleotide sequence of the promoter DNA itself contains this information; therefore, if the transcription start point is known, the promoter type and the pattern of its protein regulation can be predicted with a high probability. The strength of the promoter is more difficult to predict, because it depends not only on specific contacts between 6 subunits and the corresponding consensus elements, but also on numerous nonspecific factors that cannot be comprehensively taken into account with the available resources. This review deals with the characteristics of contacts formed by RNA polymerase a subunits, which apparently do not involve functional groups of bases. Attempts are made to compare the nucleotide sequences of promoters of different types at potential a-subunit binding sites and to discuss the possible role of this interaction in transcription regulation.