RNA POLYMERASE SENSES PERIODICITIES IN THE PROMOTER STRUCTURE

Kutuzova G. I., Frank G. K., Esipova N. G.
A.N. Bach Institute of Biochemistry, Russian Academy of Science, Moscow, Russia; V.A. Engelgardt Institute of Molecular Biology, Russian Academy of Science, Moscow, Russia.
The results derived by detection and analysis of periodicities in the primary structure of DNA are important for understanding of regularities of higher-order DNA structures formation and stability. RNA polymerase interacts with many DNA regions despite of great variability of their primary structures. So RNA polymerase can recognize not only local but also global peculiarities of the DNA structure reflected in periodicities of nucleotides and nucleotide groups in the nucleotide sequence. We suppose that analysis of periodicities in the primary structure of individual promoters may yield some clues to the problem of the RNA polymerase-promoter interaction.

The Fourier spectra of more then 400 E.coli DNA promoter sequences have been obtained with the aid of Matrix Fourier analysis [Makeev & Tumanyan, 1996] using the computer program PERF. The typical and individual properties of these spectra were analyzed. We observed wide diversity in the Fourier spectra of different promoters. The Fourier spectra of promoter sequences were compared with that of adjacent to them regions of DNA. We observed differences between Fourier spectrum of a given promoter sequence and Fourier spectra of adjacent to it DNA regions.

The relation between promoter nucleotide sequence periodicities and promoter efficiency has been established.

We found also periodicities in the RNA polymerase contacts on the promoters lacUV5, tetR, T7 A3, RNA1, trp S.t., lambda cinand lambda c17 on the basis of the results of protection and premodification experiments from [Chenchick et al., 1981, Duval-Valentin et al., 1986]. The comparison of periodicities in contacts of core RNA polymerase on the lacUV5 promoter and that of holoenzyme on the basis of experimental data from [Chenchick et al., 1981] revealed more prominent 7-fold periodicity in Fourier-spectrum of the holoenzyme contacts. Comparison of the Fourier spectra of the RNA polymerase contacts on seven different promoters revealed that despite of diversity of these spectra, they share some common features. It is possible that RNA polymerase recognizes specific periodic pattern in the promoter structure.

This work was supported by Russian Foundation for Basic Research grant N 97-04-49707.

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