Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

New Insights into Protein-DNA Electrostatic interactions: Beyond Promoters to Transcription Factors Binding Sites

Electrostatic properties of genome DNA are well recognized to influence its interactions with different proteins such as histones (1, 2), and in particular the primary recognition and regulation of transcription by RNA-polymerase. This enzyme may identify promoters and evaluate their strength due to the peculiarity of their electrostatic profiles (3-7). The same problem of recognition of a limited number of specific sequences in the long DNA molecule faces also transcription factors. To reveal the role of electrostatic properties here we studied binding sites of different families of these proteins.

The analysis of the profiles using DEPPDB – DNA Electrostatic Potential Properties Database – showed a number of common features, which can be illustrated with the cAMP-CRP complex binding sites in the genome DNA in E.coli K12 (fig. 1).

Figure 1: Averaged electrostatic profile of the cAMP-CRP complex binding sites in the genome DNA in E.coli K12 (above) and the GC content (below). The binding site consensus region is highlighted with gray.

The averaged profiles of the DNA electrostatic potential aligned around the CRP dimer binding sites centers exhibit the pronounced rise in the negative potential value with the characteristic W-like profile in the concensus area of 16 bp (TGTGA-N6-TCACA palindrome). The extensive (around 150-300 bp long), symmetrical overall potential rise can not be explained by the influence of the concensus itself and reflects the sequence organization of the flanking regions, contributing to the high potential area formation. Apparently this sequence organization was selected evolutionary to support the binding site recognition by the regulation protein molecule and its retention.

It is worth noting that this high potential area is relatively AT-enriched though doesn't possess any textual consensus properties. Such enrichment is commonly accepted as facilitating the DNA melting in the promoter regions. However, it is clearly not the case in the present system, as the promoter core (and the initially DNA melting point) lies downstream of the CRP binding sites, sometimes more than 100 bp apart. So the function of this enrichment is rather the formation of the high electrostatic potential trap for the CRP complex, especially given the fact of the symmetry of this electrostatic valley, which wouldn't be the case if due to the promoter core influence.

The same overall properties, though vary in particular details, are typical to binding sites of other families of transcription factors in a diverged range of bacterial taxa.

The data obtained reveal the role of electrostatic properties of DNA in the recognition of the transcription regulation proteins binding sites, further confirming their universal importance in the protein-DNA interactions beyond the classical promoter-RNA polymerase recognition and regulation. They demonstrate the necessity of the studies of the electrostatic properties of genome DNA in addition to the traditional textual analysis of its sequence.


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Eugenia A. Krutinina
Gleb G. Krutinin
Svetlana G. Kamzolova
Alexander A. Osypov*

Institute of Cell Biophysics
Russian Academy of Sciences
Pushchino Moscow Region, 142290