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Bacteriophage λ: Electrostatic properties of the genome and its elements

  • Molecular Phylogenetics
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Abstract

Bacteriophage λ is a classical model object in molecular biology, but little is still known on the physical properties of its DNA and regulatory elements. A study was made of the electrostatic properties of phage λ DNA and regulatory elements. A global electrostatic potential distribution along the phage genome was found to be nonuniform with main regulatory elements being located in a limited region with a high potential. The RNA polymerase binding frequency on the linearized phage chromosome directly correlates with its local potential. Strong promoters of the phage and its host Escherichia coli have distinct electrostatic upstream elements, which differ in nucleotide sequence. Attachment and recombination sites of phage λ and its host have a higher potential, which possibly facilitates their recognition by integrase. Phage λ and host Rho-independent terminators have a symmetrical M-shaped potential profile, which only slightly depends on the annotated terminator palindrome length, and occur in a region with a substantially higher potential, which may cause polymerase retention, facilitating the formation of a terminator hairpin in RNA. It was concluded that virtually all elements of phage λ genome have potential distribution specifics, which are related to their structural properties and may play a role in their biological function. The global potential distribution along the phage λ genome reflects the architecture of the regulation of its transcription and integration in the host genome.

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References

  1. Polozov R.V., Dzhelyadin T.R., Sorokin A.A., Ivanova N.N., Sivozhelezov V.S., Kamzolova S.G. 1999. Electrostatic potentials of DNA. Comparative analysis of promoter and nonpromoter nucleotide sequences. J. Biomol. Struct. Dyn. 16(6), 1135–1143.

    Article  CAS  PubMed  Google Scholar 

  2. Nechipurenko Yu.D., Nechipurenko D.Yu., Il’icheva I.A., Golovkin M.V., Panchenko L.A., Polozov R.V., Grokhovskii S.L. 2010. Conformationdynamic properties of DNA and approaches to physical mapping of the genome. Komp’yut. Issled. Model. 2(4), 419–428.

    Google Scholar 

  3. Kamzolova S.G., Sorokin A.A., Dzhelyadin T.D., Beskaravainy P.M., Osypov A.A. 2005. Electrostatic potentials of E. coli genome DNA. J. Biomol. Struct. Dyn. 23(3), 341–345.

    CAS  PubMed  Google Scholar 

  4. Florquin K., Saeys Y., Degroeve S., Rouzé P., Van de Peer Y. 2005. Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Res. 33(13), 4255–4264.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  5. Kamzolova S.G., Sorokin A.A., Osipov A.A., Beskaravainy P.M. 2009. Electrostatic map of bacteriophage T7 genome. Comparative analysis of electrostatic properties of σ70-specific T7 DNA promoters recognized by Escherichia coli RNA polymerase. Biofizika. 54(6), 975–983.

    CAS  PubMed  Google Scholar 

  6. Pedone F., Mazzei F., Santoni D. 2004. Sequence-dependent DNA torsional rigidity: A tetranucleotide code. Biophys. Chem. 112(1), 77–88.

    Article  CAS  PubMed  Google Scholar 

  7. Dineen D.G., Wilm A., Cunningham P., Higgins D.G. 2009. High DNA melting temperature predicts transcription start site location in human and mouse. Nucleic Acids Res. 7(22), 7360–7367.

    Article  Google Scholar 

  8. Petri V., Hsieh M., Jamison E., Brenowitz M. 1998. DNA sequence-specific recognition by the Saccharomyces cerevisiae “TATA” binding protein: Promoterdependent differences in the thermodynamics and kinetics of binding. Biochemistry. 37(45), 15842–15849.

    Article  CAS  PubMed  Google Scholar 

  9. Pérez-Martín J., Rojo F., de Lorenzo V. 1994. Promoters responsive to DNA bending: A common theme in prokaryotic gene expression. Microbiol. Rev. 58(2), 268–290.

    PubMed Central  PubMed  Google Scholar 

  10. Borowiec J.A., Gralla J.D. 1987. All three elements of the lac ps promoter mediate its transcriptional response to DNA supercoiling. J. Mol. Biol. 195(1), 89–97.

    Article  CAS  PubMed  Google Scholar 

  11. Kamzolova S.G., Sivozhelezov V.S., Sorokin A.A., Dzhelyadin T.R., Ivanova N.N., Polozov R.V. 2000. RNA polymerase-promoter recognition. Specific features of electrostatic potential of “early” T4 phage DNA promoters. J. Biomol. Struct. Dyn. 18(3), 325–334.

    Article  CAS  PubMed  Google Scholar 

  12. von Hippel P.H. 2004. Biochemistry. Completing the view of transcriptional regulation. Science. 305(5682), 350–352.

    Article  Google Scholar 

  13. Kamzolova S.G., Beskaravainy P.M., Osypov A.A., Dzhelyadin T.R., Temlyakova E.A., Sorokin A.A. 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.

    Article  CAS  PubMed  Google Scholar 

  14. Kalodimos C.G., Biris N., Bonvin A.M., Levandoski M.M., Guennuegues M., Boelens R., Kaptein R. 2004. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science. 305(5682), 386–389.

    Article  CAS  PubMed  Google Scholar 

  15. Sorokin A.A., Osypov A.A., Dzhelyadin T.R., Beskaravainy P.M., Kamzolova S.G. 2006. Electrostatic properties of promoter recognized by E. coli RNA polymerase E sigma70. J. Bioinform. Comput. Biol. 4 (2), 455–467.

    Google Scholar 

  16. Krutinina E.A., Krutinin G.G., Kamzolova S.G., Osypov A.A. 2011. New insights into protein-DNA electrostatic interactions: Beyond promoters to transcription factors binding sites. J. Biomol. Struct. Dyn. 28(6), 1137–1138.

    Google Scholar 

  17. McGrath S., van Sinderen D. 2007. Bacteriophage: Genetics and Molecular Biology. Norfolk, UK: Caister Acad. Press.

    Google Scholar 

  18. Osypov A.A., Krutinin G.G., Kamzolova S.G. 2010. DEPPDB-DNA electrostatic potential properties database: Electrostatic properties of genome DNA. J. Bioinform. Comput. Biol. 8(3), 413–425.

    Article  CAS  PubMed  Google Scholar 

  19. Osypov A.A., Krutinin G.G., Krutinina E.A., Kamzolova S.G. 2012. DEPPDB-DNA electrostatic potential properties database: Electrostatic properties of genome DNA elements. J. Bioinform. Comput. Biol. 10(2), 1241004.

    Article  PubMed  Google Scholar 

  20. Campbell A. 2007. Phage integration and chromosome structure. A personal history. Annu. Rev. Genet. 41, 1–11.

    Article  CAS  PubMed  Google Scholar 

  21. Krutinin G.G., Krutinina E.A., Kamzolova S.G, Osypov A.A. 2011. The role of electrostatics in protein-DNA interactions in phage lambda. J. Biomol. Struct. Dyn. 28(6). 1139.

    Google Scholar 

  22. Krutinina E.A., Krutinin G.G., Kamzolova S.G., Osypov A.A. 2014. Electrostatics of prokaryotic transcription factors match that of their binding sites. FEBS J. 281(Suppl. 1), 682.

    Google Scholar 

  23. Harada Y., Funatsu T., Murakami K., Nonoyama Y., Ishihama A., Yanagida T. 1999. Single-molecule imaging of RNA polymerase-DNA interactions in real time. Biophys. J. 76(2), 709–715.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  24. Kamzolova S.G., Sorokin A.A., Beskaravainy P.M., Osypov A.A. 2005. Comparative analysis of electrostatic patterns for promoter and non promoter DNA. In: E. coli, Bioinformatics of Genome Regulation and Structure II. Eds. Kolchanov N., Hofestaedt R. New York: Springer.

    Google Scholar 

  25. Osypov A.A., Krutinin G.G., Krutinina E.A., Kamzolova S.G. 2014. Electrostatic properties of natural DNA palindromes: Transcription factors binding sites and terminators. FEBS J. 281(Suppl. 1), 681.

    Google Scholar 

  26. Sorokin A.A., Osipov A.A., Beskaravainy P.M., Kamzolova S.G. 2007. Analysis of the nucleotide sequence and electrostatic potential distribution in the Escherichia coli genome. Biophysics (Moscow). 52(2), 168–171.

    Article  Google Scholar 

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Authors and Affiliations

  1. Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russia

    G. G. Krutinin, E. A. Krutinina, S. G. Kamzolova & A. A. Osypov

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  1. G. G. Krutinin
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  2. E. A. Krutinina
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  3. S. G. Kamzolova
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  4. A. A. Osypov
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Correspondence to A. A. Osypov.

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Original Russian Text © G.G. Krutinin, E.A. Krutinina, S.G. Kamzolova, A.A. Osypov, 2015, published in Molekulyarnaya Biologiya, 2015, Vol. 49, No. 3, pp. 384–393.

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Krutinin, G.G., Krutinina, E.A., Kamzolova, S.G. et al. Bacteriophage λ: Electrostatic properties of the genome and its elements. Mol Biol 49, 339–347 (2015). https://doi.org/10.1134/S0026893315030115

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  • DOI: https://doi.org/10.1134/S0026893315030115

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