Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

The Dependency of Promoter Strength upon the Electrostatic Up-element in E.coli rrnB P1 Promoter Mutants

It is known that not only the consensus sequence text is essential for RNA polymerase-promoter recognition and regulation, but physical properties, especially electrostatics, play important role particularly at the early stages of this process. One of the elements that may play a crucial role in the promoter strength regulation is a so-called "up-element", which interacts with the alpha-subunit of RNAP and thus facilitates its binding to the promoter. There is no text consensus in the "up-element" (though high AT content is often attributed) and functionality of this region is defined by its physical properties. We have shown earlier, that electrostatics is responsible for its functioning during the global transcription switch under the T4 bacteriophage infection and that strong T4, early T7-like, phage Lambda and E.coli ribosomal promoters with pronounced up-element have high levels of the electrostatic potential within it.


Electrostatic profiles of the up-elements of E.coli ribosomal rrnB P1 promoter mutants, aligned around their centers. The areas up- and downstream of the shown up-elements have the same electrostatic profile (and the sequence text) within all given promoters. Red profile - eliminated up-element promoter with zero strength. Green - the strongest promoter.

Vertical axe: electrostatic potential in ē/Å. Horizontal axe: sequence length in Å aligned around centers of proximal parts of up-elements (red vertical line). The -35 promoter element is marked gray. Horizontal line - average for the whole E.coli genome.

Here we demonstrate that, taken from [Estrem et al.], in the strong E.coli ribosomal rrnB P1 promoter and its up-element mutants the promoter strength depends upon the size of the electrostatic up-element so that the bigger the element - the stronger the promoter is. However, if the element is too big the strength decreases slightly due to possible over-sticking (trapping) of the polymerase.

DEPPDB (deppdb.psn.ru) and its tools were used to make the analysis. This research has been supported by RFBR grant 14-44-03683.

    S.G. Kamzolova, A.A. Sorokin, T.D. Dzhelyadin P.M., Beskaravainy, A.A. Osypov. (2005) Electrostatic potentials of E. coli genome DNA, J. Biomol. Struct. Dyn. 23(3), 341-346.

    A. A. Osypov, G.G. Krutinin, S. G. Kamzolova. (2010) DEPPDB - DNA Electrostatic Potential Properties Database. Electrostatic Properties of Genome DNA, J Bioinform Comput Biol, 8(3), 413-25

    A. A. Osypov, G.G. Krutinin, E.A. Krutinina, S. G. Kamzolova. (2012) DEPPDB - DNA Electrostatic Potential Properties Database. Electrostatic Properties of Genome DNA elements, J Bioinform Comput Biol, 10(2) 1241004

    G.G. Krutinin, E.A. Krutinina, S. G. Kamzolova, A. A. Osypov. (2011) The Role of Electrostatics in Protein-DNA Interactions in Phage Lambda, J Biomol Struct Dyn, 28(6), 1139-1140

    S.T. Estrem, T. Gaal, W. Ross, R.L. Gourse. (1998) Identification of an UP element consensus sequence for bacterial promoters, Proc Natl Acad Sci U S A 95(17), 9761-9766

    S.T. Estrem, W. Ross, T. Gaal, Z.W. Chen, W. Niu, R.H. Ebright, R.L. Gourse. (1999) Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit, Genes Dev 13(16), 2134-2147

    N. Abe, M. Slattery, I. Dror, R. Rohs, B. Honig, R.S. Mann. (2013) Deconvoluting the recognition of DNA shape from DNA sequence, J. Biomol. Struct. Dyn. 31 SI Supplement: 1 43-43.

    D. Guo, Sh. Liu, Y. Huang, Yi Xiao. (2013) Preorientation of protein and RNA just before contacting, J. Biomol. Struct. Dyn. 31(7), 716-728

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

Institute of Cell Biophysics of RAS
Pushchino Moscow Region, Russia, 142290

Ph: +7(929) 606-9828