Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Electrostatic Potential Map of the Whole Genome DNA of T7 Bacteriophage. Electrostatic Properties and Function of its Promoter Regions

Promoter recognition and open complex formation are central events in the initiation of transcription by RNA-polymerase and are shown to be affected by electrostatic properties of promoter DNA. It was shown also that electrostatic properties of promoter sequences differ from that of coding regions.

Here we calculated the electrostatic potential profile of the whole genome DNA of bacteriophage T7 and draw electrostatic potential map of the whole genome and its promoter regions. Some observations are also made concerning electrostatic properties of promoters in respect to their biological functions.

Promoters of T7 bacteriophage are recognized by the two forms of RNA-polymerase - the major form of RNA-polymerase (Es70) of Escherichia coli serves the early genes, while RNA-polymerase of the phage itself takes care of the late genes. During the first few minutes after infection of E. coli by the bacteriophage T7, transcription is dependent on the host's RNA polymerase and is confined to the "early" operon at the "left" end of the genome. Three classes of T7 genes have been recognized according to their expression time. The functions of class I genes are mainly to subvert the bacterium into a phage-producing factory; the only essential phage gene is gene 1, coding for the T7 RNA polymerase, which transcribes the class II genes, mainly involved in phage DNA metabolism, and the class III genes, whose functions are predominantly morphogenetic.

Synthesis of a mRNA begins before the entire region of DNA coding for that mRNA has entered the cell and entry of ~97 percent of T7 DNA is driven by transcribing RNA polymerase. Class I genes are transcribed by E.coli RNAP which recognizes three promoters (A1-A3, B and C) positioned near the leading end of T7 DNA. Their electrostatic properties differ from that of most class II and III genes. They are more structurally expressed and possess a somehow classical look of peaks and valleys of a typical promoter. A2 and A3 are ~25% as active as A1 which correlates with their electrostatic properties, where the A1 is the most prominent of them. In the contrary, promoters of class II and III genes exhibit more diverse appearance, ranging from rather classical look through a more or less definite, though not common, electrostatic patterns to many of them being completely indistinguishable from ordinary coding regions. It was shown that during the phage infection pH becomes higher and that T7 RNAP has higher pH optimum then that of E.coli. It is reasonable to conclude then, that the difference in the electrostatic properties of the DNA molecule in the more alkaline conditions may affect its promoter properties. This indicates the necessity of further investigations including modification of the calculating method to accommodate different intracellular conditions.


The authors are grateful to Saveljeva E. G. for technical support.

References and Footnotes
  1. Dunn J. J., Studier F. W., Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements, J. Mol. Biol., 166(4), 477-535 (1983)
  2. Boothroyd J. C., Hayward R. S., New genes and promoters suggested by the DNA sequence near the end of the coliphage T7 early operon, Nucleic Acids Res., 7(7), 1931-1943 (1979)
  3. Kamzolova S. G., Sivozhelezov V. S., Sorokin A. A.,. Dzhelyadin T. R, Ivanova N. N., Polozov R. V., RNA polymerase- promoter recognition. Specific features of electrostatic potential of "early" T4 phage DNA promoters, J. Biomol. Struct. Dyn., 18(3), 325-334 (2000).
  4. Kamzolova S.G., Sorokin A.A., Dzhelyadin T.D., Beskaravainy P.M., Osypov A.A., Electrostatic potentials of E.coli genome DNA. J. Biomol. Struct. Dyn., v.23(3), 341-346 (2005).

Alexander A. Osypov
Petr M. Beskaravainy
Anatoly A. Sorokin
Svetlana G. Kamzolova

Institute of Cell Biophysics of RAS, Pushchino, Moscow region, Russia

Email: ao@icb.psn.ru
Email: kamzolova@icb.psn.ru