RNA polymerase senses periodicities in the promoter structure
Kutuzova G.I.1, Frank G.K. and Esipova N.G.
1A.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 cin
and
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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- Chenchick, A., Beabealashvilli, R., Mirzabekov, A. 1981. Topography
of interaction of Escherichia coli RNA polymerase subunits with lac UV5
promoter. FEBS Lett. 128, 46-50.
- Duval-Valentin, Guy and Ehrlich, R. 1986. Interaction between E.coli
RNA polymerase and tetR promoter from pSC101: homologies and differences
with other E.coli promoter systems from close contact point studies. 14,
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