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Albany 2015:Book of Abstracts

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

Electrostatic properties of T7-like phages promoters for host bacterial and native viral RNA polymerases

It is known that not only the consensus sequence text is essential for RNA polymerase-promoter recognition, but some additional information can be coded in physical properties of DNA. Especially electrostatic interactions between promoter DNA and RNA polymerase is of considerable importance in regulating promoter function.

Considering organization of genome of some T7-like phages there are two main regions and consequently two main promoter types: the early region is transcribed by bacterial host RNA polymerase and possess a tandem of two or three strong promoters. One of the main products of this region is the native viral RNA polymerase, which transcribes all the next region. Bacterial polymerases are big proteins with several subunits and have the landing region of some 150 b.p., while viral are small and consist of one subunit with the landing region of some 25 b.p., which a priori suggests different characteristics of their interactions with promoter DNA.

Using DEPPDB - DNA Electrostatic Potential Properties Database- we compared electrostatic properties of promoters for host bacterial and native viral RNA polymerases. The electrostatic profile for bacterial promoters exhibit strong elements of large amplitude spanning for some hundreds base pairs (Fig. 1), while that of promoters for viral RNA polymerase show considerable and consensus similarity in the region of some two-three tens base pairs only (Fig. 2), which closely resemble the physical properties of the two kinds of enzymes.

The similarity between T7, T3, phiA1122, phiYeO3-12, K1-5 SP6 suggests the presence and activity of the early host promoters for phiYeO3-12, for which non-experimental evidence only is given in the NCBI RefSeq Database and for K1-5, SP6 phiA1122, for which there are no annotations there.

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Fig. 1. Distribution of electrostatic potential around 500 b.p. of T7, T3, phiA1122, phiYeO3-12 early region (aligned at 501 position) and K1-5, SP6 early region (aligned at 567 and 501 positions). Grey- individual profiles, black - averaged. Vertical axe: electrostatic potential in ē/Å. Horizontal axe: sequence length in Å aligned around mentioned positions (vertical line).

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Fig. 2. Distribution of electrostatic potential around 50 b.p. (averaged by genomes, left) or 500 b.p. (averaged all, right) of T7, T3, phiYeO3-12, VP4 native phage polymerase promoters: 1. T7 promoters (17 pos.); 2. T3 promoters (14 pos.); 3. phiYeO3-12 promoters (15 pos.); 4. VP4 promoters (14 pos.). Vertical axe: top - electrostatic potential in ē/Å. bottom - group standard deviation. Horizontal axe: sequence length in E aligned around start point (vertical line).

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

References
    SG Kamzolova, PM Beskaravainy, AA Osypov, TR Dzhelyadin, EA Temlyakova, AA Sorokin, (2014), Electrostatic map of T7 DNA: comparative analysis of functional and electrostatic properties of T7 RNA polymerase-specific promoters, J Biomol Struct Dyn, 32(8), 1184-1192

    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


Alexander A. Osypov*
Svetlana G. Kamzolova

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

Ph: +7(929) 606-9828
aosypov@gmail.com