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Albany 2015:Book of Abstracts

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

Genetic and Electrostatic Maps of Bacteriophage Lambda Genome

Bacteriophage lambda is a classical model object and its genome is extensively studied. However, little is known about physical properties of its genome and its elements. Here for the first time we study their electrostatic potential properties.

Electrostatic potential global distribution along lambda phage. genome corresponds to the localization of its main regulatory elements in the restricted area with high negative electrostatic potential, which is higher than E.coli host average. Binding frequency of RNA polymerase to DNA along the genome, measured in direct experiment, correlates to the calculated electrostatic potential. Strong promoters, as pL and pR in lambda and lambda-like phages, early promoters in T7-like phages, and E.coli ribosomal promoters have strong electrostatic up-elements, the sequence texts of which are quite different. Strong E.coli promoters with eliminated up-element (and thus having greatly reduced strength) have no pronounced electrostatic potential valleys in the corresponding area. Mutated up-elements with enhanced promoter strength exhibit deep electrostatic potential valleys and peculiarities of some other physical properties. This may indicate the direct role of electrostatic potential in promoters functioning.

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Attachment sites of phage lambda and E.coli have high electrostatic potential for integrase recognition. Rho independent lambda and E.coli terminators have the same M-like electrostatic potential profile, reflecting their palindrome nature, with the same electrostatic potential scale in three-fold different annotated palindrome length. Rho dependent terminators have no common electrostatic potential.

Almost all lambda genome elements exhibit electrostatic potential peculiarities of different kind, that reflect their structural properties and may play role in their biological functioning. Overall genome electrostatic potential reflects its transcription and host-integration regulation architecture.

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

References
    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.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


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