0026-8933/04/3805- © 2004 MAIK “Nauka / Interperiodica” 0663 Molecular Biology, Vol. 38, No. 5, 2004, pp. 663–673. Translated from Molekulyarnaya Biologiya, Vol. 38, No. 5, 2004, pp. 786–797. Original Russian Text Copyright © 2004 by Ozoline, Purtov, Brok-Volchanski, Deev, Lukyanov. INTRODUCTION The unprecedented degenerateness of conserved bacterial promoter elements obviously complicates their recognition by RNA polymerase using the stan- dard algorithm. However, it also lays the basis for dif- ferential expression of several thousands of genes and facilitates manifestation of various regulatory mecha- nisms. This is the most probable reason why only one vegetative promoter in the Escherichia coli genome contains all of the 12 conserved pairs (metY-P1), and even in this case the spacer between consensus ele- ments is not optimal. Most promoters contain only seven or eight conserved pairs. In bacterial DNA, the number of sites that exhibit this degree of similarity to conserved elements is one or two orders of magnitude larger than the number of genes. Therefore, a certain correspondence to the consensus is a necessary but not sufficient condition for the formation of a productive complex with RNA polymerase, and nucleotide sequences of real promoters should contain elements increasing the probability of their recognition by this enzyme. These include elements ensuring the DNA conformation optimal for the formation of the tran- scription complex; however, transcription selectivity mainly depends on the elements in direct contact with RNA polymerase or transcription regulators. RNA polymerase with the proper polypeptide composition is certainly the most important factor determining the efficiency of transcription of a given gene. Under vegetative growth conditions, the enzyme containing the protein product of gene rpoD–σ D as a promoter specificity factor prevails in bacterial cells. This polymerase can interact with most bacterial pro- moters and transcribe almost all genes. In addition to σ D , six other σ subunits have been found in E. coli: σ S , σ H , σ E , σ F , σ N , and σ FecI [1]. They replace σ D in the complex with the core enzyme and recognize base sequences specific to them. The cell needs alternative σ subunits at certain developmental stages (σ S ) and under different stress conditions (σ E , σ H , and σ S ); however, the polymerases containing these factors also transcribe some operons during normal growth. For example, the cellular content of σ D is comparable to those of σ N and σ F [2], which control the expression of a comparatively small number of genes. The rela- tive amounts of different σ factors is determined by the efficiency of the corresponding gene transcription, the stability of their RNA and protein products, and the presence of anti-σ factors (Rsd, RseA, FlgM, FecR, and DnaJ–DnaK for σ D , σ E , σ F , σ EecI , and σ H , respectively) [3–6]. The genes whose intense expres- sion is required under different conditions usually Specificity of DNA–Protein Interactions within Transcription Complexes of Escherichia coli O. N. Ozoline 1 , Yu. A. Purtov 1 , A. S. Brok-Volchanski 1 , A. A. Deev 2 , and V. I. Lukyanov 1 1 Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia; E-mail: ozoline@mail.icb.psn.ru 2 Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia Received November 18, 2003 Abstract—The identification of DNA–protein and protein–protein contacts in transcription complexes is a nec- essary 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 σ 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 σ subunits and the corresponding consensus elements, but also on numerous nonspecific factors that cannot be compre- hensively taken into account with the available resources. This review deals with the characteristics of contacts formed by RNA polymerase α 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 α-subunit binding sites and to discuss the possible role of this interaction in transcription regulation. Key words: promoter, RNA polymerase, conserved elements, alternative σ factors, α subunit, Escherichia coli UDC 577.15.03 DNA–PROTEIN INTERACTIONS