Molecular Biology

, Volume 52, Issue 5, pp 686–692 | Cite as

Destabilization of the DNA Duplex of Actively Replicating Promoters of T7-Like Bacteriophages

  • M. A. Orlov
  • A. A. Ryasik
  • A. A. Sorokin

Abstract—The relation between the processes of replication and transcription has been actively studied over several decades, but detailed mechanisms for their interaction have not been established reliably. Among the initiating transcription promoters of bacteria and bacteriophages, there are both promoters having an additional function of the secondary origin of replication (OR) and promoters not participating in this process. In this paper, we describe the stability of DNA by Stress-Induced Duplex Destabilization (SIDD) profiles for a complete set of promoters and the primary OR of the bacteriophage T7 genome. It has been shown that, among the native T7 promoters, only those that have an additional function of secondary OR are characterized by high destabilization. These include the phiOL and phiOR promoters adjoining the 5' and 3' terminal repeats of bacteriophage T7, and of six other T7 group phages. In each case, these two promoters are located in the regions of DNA with high destabilization of the duplex. Additionally, the genomes of seven representatives of the T7 group without annotated phiOL and phiOR have been considered. For three of them, high peaks of SIDD profiles have been found near the ends of the genomic DNA that may be due to the presence of similar phiOL and phiOR promoters. Probably, such promoters can be found in the genomes of other bacteriophages. Thus, for the promoters of bacteriophages, we have a confirmation of the relationship of SIDD as a DNA duplex parameter and the DNA replication initiation on promoters, serving as secondary OR.


DNA physics DNA replication DNA transcription bacteriophage T7 SIDD 



  1. 1.
    Lark K.G. 1972. Evidence for the direct involvement of RNA in the initiation of DNA replication in Escherichia coli 15T. J. Mol. Biol. 64 (1), 47–60.CrossRefPubMedGoogle Scholar
  2. 2.
    Kornberg A., Baker T.A. 1992. Replication mechanisms and operations. In: DNA Replication, 2nd ed. New York: Freeman, pp. 471–510.Google Scholar
  3. 3.
    Baker T.A., Kornberg A. 1988. Transcriptional activation of initiation of replication from the E. coli origin: An RNA–DNA hybrid near oriC. Cell. 55, 113–123.CrossRefPubMedGoogle Scholar
  4. 4.
    Keppel F., Fayet O., Georgopoulos C. 1988. Strategies of bacteriophage DNA replication. In: The Bacteriophages, vol. 2. Ed. Calendar R. New York: Plenum, pp. 145–264.Google Scholar
  5. 5.
    Hinkle D.C. 1980. Evidence for direct involvement of T7 RNA polymerase bacteriophage DNA replication. J. Virol. 34 (1), 136–141.PubMedPubMedCentralGoogle Scholar
  6. 6.
    Zhang X., Studier F.W. 2004. Multiple roles of T7 RNA polymerase and T7 lysozyme during bacteriophage T7 infection. J. Mol. Biol. 340 (4), 707–730.CrossRefPubMedGoogle Scholar
  7. 7.
    Zhang X., Studier F.W. 1995. Isolation of transcriptionally active mutants of T7 RNA polymerase that do not support phage growth. J. Mol. Biol. 250, 156–168.CrossRefPubMedGoogle Scholar
  8. 8.
    Moffatt B.A., Studier F.W. 1987. T7 lysozyme inhibits transcription by T7 RNA polymerase. Cell. 49, 221–227.CrossRefPubMedGoogle Scholar
  9. 9.
    Cheng X., Zhang X., Pflugrath J.W., Studier F.W. 1994. The structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 91, 4034–4038.CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Dunn J.J., Studier F.W. 1983. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 166, 477–535.CrossRefPubMedGoogle Scholar
  11. 11.
    Rabkin S.D., Richardson C.C. 1988. Initiation of DNA replication at cloned origins of bacteriophage T7. J. Mol. Biol. 204, 903–916.CrossRefPubMedGoogle Scholar
  12. 12.
    Romano L.J., Tamanoi F., Richardson C.C. 1981. Initiation of DNA replication at the primary origin of bacteriophage T7 by purified proteins: Requirement for T7 RNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 78, 4107–4111.CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Sugimoto K., Kohara Y., Okazaki T. 1987. Relative roles of T7 RNA polymerase and gene 4 primase for the initiation of T7 phage DNA replication in vivo. Proc. Natl. Acad. Sci. U. S. A. 84, 3977–3981.CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Studier F.W. 1969. The genetics and physiology of bacteriophage T7. Virology. 39, 562–574.CrossRefPubMedGoogle Scholar
  15. 15.
    Kelly T.J., Jr, Thomas C.A., Jr. 1969. An intermediate in the replication of bacteriophage T7 DNA molecules. J. Mol. Biol. 44, 459–475.CrossRefPubMedGoogle Scholar
  16. 16.
    Chung Y.B., Hinkle D.C. 1990. Bacteriophage T7 DNA packaging: 2. Analysis of the DNA sequences required for packaging using a plasmid transduction assay. J. Mol. Biol. 216, 927–938.CrossRefPubMedGoogle Scholar
  17. 17.
    Hashimoto C., Fujisawa H. 1992. Transcription dependence of DNA packaging of bacteriophages T3 and T7. Virology. 191, 246–250.CrossRefPubMedGoogle Scholar
  18. 18.
    Kim J.S., Kim S.H., Chung Y.B. 1997. Defects in concatemer processing of bacteriophage T7 DNA deleted in the M-hairpin region. Virology. 236, 37–46.CrossRefPubMedGoogle Scholar
  19. 19.
    Chung Y.B., Hinkle D.C. 1990. Bacteriophage T7 DNA packaging: 1. Plasmids containing a T7 replication origin and the T7 concatemer junction are packaged into transducing particles during phage infection. J. Mol. Biol. 216, 911–926.CrossRefPubMedGoogle Scholar
  20. 20.
    Fuller C.W., Richardson C.C. 1985. Initiation of DNA replication at the primary origin of bacteriophage T7 by purified proteins. Site and direction of initial DNA synthesis. J. Biol. Chem. 260, 3185 –3196.PubMedGoogle Scholar
  21. 21.
    Kamzolova S.G., Beskaravainy R.M., Osipov 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, 1184–1192.CrossRefPubMedGoogle Scholar
  22. 22.
    Bi C.-P., Benham C.J. 2004. WebSIDD: Server for predicting of the stress-induced duplex destabilized (SIDD) sites in superhelical DNA. Bioinformatics. 20, 1477–1479.CrossRefPubMedGoogle Scholar
  23. 23.
    Ak P., Benham C.J. 2005. Susceptibility to superhelically driven DNA duplex destabilization: A highly conserved property of yeast replication origins. PLoS Comput. Biol. 1, 41–46.CrossRefGoogle Scholar
  24. 24.
    Benham C.J. 1996. Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol. 255, 425–434.CrossRefPubMedGoogle Scholar
  25. 25.
    Wang H., Noordewier M., Benham C.J. 2004. Stress-induced DNA duplex destabilization (SIDD) in the Escherichia coli Genome: SIDD sites are closely associated with promoters. Genome Res. 14, 1575–1584.CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Kowalski D., Natale D.A., Eddy M.J. 1988. Stable DNA unwinding, not breathing, accounts for single-strand-specific nuclease hypersensitivity of specific A + T-rich sequences. Proc. Natl. Acad. Sci. U. S. A. 85, 9464–9468.CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    van den Berg J., Boersma A.J., Poolman B. 2017. Microorganisms maintain crowding homeostasis. Nat. Rev. Microbiol. 15, 309–318.CrossRefPubMedGoogle Scholar
  28. 28.
    Benham C.J., Bi C.-P. 2004. The analysis of stress-induced duplex destabilization in long genomic DNA sequences. J. Comput. Biol. 11, 519–543.CrossRefPubMedGoogle Scholar
  29. 29.
    Osypov A.A., Kamzolova S.G. 2015. Electrostatic properties of T7-like phages promoters for host bacterial and viral RNA polymerases. J. Biomol. Struct. Dyn. 33, 19–20.CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2018

Authors and Affiliations

  1. 1.Institute of Cell Biophysics, Russian Academy of SciencesPushchinoRussia

Personalised recommendations