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Albany 2015:Book of Abstracts

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

Electrostatic Properties of Rho-dependent and Rho-independent Terminators

Electrostatic properties of genome DNA are important to its interactions with different proteins, in particular -RNA polymerase.

It was shown earlier that higher electrostatic potential values and some peculiarities play substantial role in the polymerase-promoter recognition. Here we describe for the first time electrostatic properties of Rho-dependent and Rho-independent terminators in E.coli and bacteriophage lambda.

Rho independent lambda and E.coli terminators have the same characteristic symmetrical M-like electrostatic potential profile in the core terminators area, reflecting their palindrome nature. Terminators sites have pronounced rise in the negative potential value around them, that spans for nearly a hundred b.p.. and clearly exceed the terminator hairpin zone. Overall they have the same electrostatic potential profile scale despite three-fold different annotated palindrome length.

The same overall properties are typical in a diverged range of bacterial taxa.

Rho dependent terminators have no common electrostatic properties.

It's worth noting that quite different underlying sequences form the same electrostatic profile that carry out their biological functions. It can be speculated that the rise of the potential in the long surrounding area, comparable with the RNA polymerase size, may lead to transcription pausing that facilitate the terminator hairpin formation.

osypov-6-fig1.gif

Fig. 1. Distribution of electrostatic potential around 300 b.p. of Rho-independent (1, 2) and Rho-dependent (3, 4) terminators in E. coli (2, 4) and bacteriophage lambda (1, 3). Vertical axe: electrostatic potential in ē/Å. Horizontal axe: sequence length in b.p. aligned around terminators centers (vertical line).

osypov-6-fig2.gif

Fig. 2. Distribution of electrostatic potential around 50 b.p. of Rho-independent terminators grouped by annotated length (shown beneath). Vertical axe: electrostatic potential in ē/Å. Horizontal axe: sequence length in b.p. aligned around terminators centers (vertical line).

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

References
    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

    V. Brendela, G.H. Hammb, E.N. Trifonov. (1986) Terminators of Transcription with RNA Polymerase from Escherichia coli: What They Look Like and How to Find Them, J. Biomol. Struct. Dyn. 3(4), 705-723.

    E. Yakubovskaya, E. Mejia, J. Byrnes, E. Hambardjieva, M. Garcia-Diaz. (2013) Put a stop to it: termination of mitochondrial transcription, J. Biomol. Struct. Dyn. 31 SI Supplement: 1 80-81. DOI: 10.1080/07391102.2013.786367

    B.P. Belotserkovskii, A.J. Neil, S.S. Saleh, J.H.S.Shin, S.M. Mirkin, P.C. Hanawalt. (2013) Transcription blockage by single-strand breaks in various sequences and the general model for transcription blockage by R-loop formation, J. Biomol. Struct. Dyn. 31 SI Supplement: 1 83-84. DOI: 10.1080/07391102.2013.786372


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
aosypov@gmail.com