Book of Abstracts: Albany 2005
Oligonucleotide Analysis of E. coli Promoters Recognized by σ70-RNA Polymerase
Recent identification of of some noncanonical determinants in E. coli promoters has opened a field for a search of new candidates for this role. A large-scale comparative analysis of oligonucleotide composition of the complete sequence of E. coli genome and its promoter sites has much potential for yielding information about all kinds of nucleotide blocks preferred by promoters that might contribute to promoter recognition.
The presence of all kinds of hexa-, hepta-, and octonucleotides in E. coli complete genome and in its 359 σ70-specific promoters was determined. A nonrandom distribution of nucleotides was found both in the complete genome and in the promoters. The complete genome and the promoters were shown to differ essentially in their oligonucleotide sets. 542 different hexanucleotides, 3237 heptanucleotides, and 13332 octonucleotides are twofold more frequent in the promoters than in the chromosome. These oligonucleotides are very large in number to consider all of them as possible sequence-specific promoter determinants.
It is interesting that AT-enriched sequences predominate in promoter oligonucleotides. Short oligoA-oligoT runs similar to those found in promoter blocks are known to induce DNA curvature, a structural feature that might contribute to promoter recognition. In addition, AT-enriched sequences are known to be ?easily melting? sites that are also predisposed to interaction with RNA polymerase. Thus, it appears reasonable to suggest that the possible functional role of some promoter oligonucleotides as new signal elements recognized by RNA polymerase can be expressed through their physical properties (such as curving and bendability, thermostability, or some others).
This work was supported by Russian Foundation for Basic Research (grant RFBR-naukograd 04-04-97275).
Anatoly A. Sorokin
Institute of Cell Biophysics of RAS