Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Jan 15;24(2):282–288. doi: 10.1093/nar/24.2.282

Distamycin-induced inhibition of formation of a nucleoprotein complex between the terminase small subunit G1P and the non-encapsidated end (pacL site) of Bacillus subtilis bacteriophage SPP1.

S Chai 1, J C Alsonso 1
PMCID: PMC145643  PMID: 8628651

Abstract

The small subunit of the Bacillus subtilis bacteriophage SPP1 terminase (G1P) forms a sequence-specific nucleoprotein complex with the SPP1 non-encapsidated end (pacL site) during initiation of DNA encapsidation. Gel mobility shift assay was used to study the G1P-pacL interaction. Distamycin, a minor groove binder that induces local distortion of the DNA, inhibits G1P-pacL complex formation. The competition of G1P with distamycin for DNA binding at the pacL site is independent of the order of addition of the reactants. Other minor groove binders, such as spermine or Hoechst 33258, which do not distort DNA, failed to compete with G1P for pacL DNA binding. Cationic metals, which generate a repertoire of DNA structures different from that caused by the minor groove binders, can partially reverse the distamycin-induced inhibition of G1P binding to pacL DNA. The major groove binder methyl green, which does not distort sequence-directed bending of pacL DNA, competes with G1P for binding at the pacL site. Our data suggest that the natural sequence-directed bend that exists within the pacL site is the architectural element that facilitates assembly of a nucleoprotein complex and hence initiation of DNA encapsidation by bacteriophage SPP1.

Full Text

The Full Text of this article is available as a PDF (166.6 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Beerman T. A., McHugh M. M., Sigmund R., Lown J. W., Rao K. E., Bathini Y. Effects of analogs of the DNA minor groove binder Hoechst 33258 on topoisomerase II and I mediated activities. Biochim Biophys Acta. 1992 May 7;1131(1):53–61. doi: 10.1016/0167-4781(92)90098-k. [DOI] [PubMed] [Google Scholar]
  2. Black L. W. DNA packaging in dsDNA bacteriophages. Annu Rev Microbiol. 1989;43:267–292. doi: 10.1146/annurev.mi.43.100189.001411. [DOI] [PubMed] [Google Scholar]
  3. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
  4. Bravo A., Alonso J. C., Trautner T. A. Functional analysis of the Bacillus subtilis bacteriophage SPP1 pac site. Nucleic Acids Res. 1990 May 25;18(10):2881–2886. doi: 10.1093/nar/18.10.2881. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Broggini M., Ponti M., Ottolenghi S., D'Incalci M., Mongelli N., Mantovani R. Distamycins inhibit the binding of OTF-1 and NFE-1 transfactors to their conserved DNA elements. Nucleic Acids Res. 1989 Feb 11;17(3):1051–1059. doi: 10.1093/nar/17.3.1051. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bruzik J. P., Auble D. T., deHaseth P. L. Specific activation of transcription initiation by the sequence-specific DNA-binding agents distamycin A and netropsin. Biochemistry. 1987 Feb 10;26(3):950–956. doi: 10.1021/bi00377a040. [DOI] [PubMed] [Google Scholar]
  7. Chai S., Bravo A., Lüder G., Nedlin A., Trautner T. A., Alonso J. C. Molecular analysis of the Bacillus subtilis bacteriophage SPP1 region encompassing genes 1 to 6. The products of gene 1 and gene 2 are required for pac cleavage. J Mol Biol. 1992 Mar 5;224(1):87–102. doi: 10.1016/0022-2836(92)90578-8. [DOI] [PubMed] [Google Scholar]
  8. Chai S., Kruft V., Alonso J. C. Analysis of the Bacillus subtilis bacteriophages SPP1 and SF6 gene 1 product: a protein involved in the initiation of headful packaging. Virology. 1994 Aug 1;202(2):930–939. doi: 10.1006/viro.1994.1415. [DOI] [PubMed] [Google Scholar]
  9. Chai S., Lurz R., Alonso J. C. The small subunit of the terminase enzyme of Bacillus subtilis bacteriophage SPP1 forms a specialized nucleoprotein complex with the packaging initiation region. J Mol Biol. 1995 Sep 29;252(4):386–398. doi: 10.1006/jmbi.1995.0505. [DOI] [PubMed] [Google Scholar]
  10. Coll M., Aymami J., van der Marel G. A., van Boom J. H., Rich A., Wang A. H. Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment. Biochemistry. 1989 Jan 10;28(1):310–320. doi: 10.1021/bi00427a042. [DOI] [PubMed] [Google Scholar]
  11. Deichelbohrer I., Messer W., Trautner T. A. Genome of Bacillus subtilis Bacteriophage SPP1: Structure and Nucleotide Sequence of pac, the Origin of DNA Packaging. J Virol. 1982 Apr;42(1):83–90. doi: 10.1128/jvi.42.1.83-90.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dorn A., Affolter M., Müller M., Gehring W. J., Leupin W. Distamycin-induced inhibition of homeodomain-DNA complexes. EMBO J. 1992 Jan;11(1):279–286. doi: 10.1002/j.1460-2075.1992.tb05050.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Griffith J., Bleyman M., Rauch C. A., Kitchin P. A., Englund P. T. Visualization of the bent helix in kinetoplast DNA by electron microscopy. Cell. 1986 Aug 29;46(5):717–724. doi: 10.1016/0092-8674(86)90347-8. [DOI] [PubMed] [Google Scholar]
  14. Klevit R. E., Wemmer D. E., Reid B. R. 1H NMR studies on the interaction between distamycin A and a symmetrical DNA dodecamer. Biochemistry. 1986 Jun 3;25(11):3296–3303. doi: 10.1021/bi00359a032. [DOI] [PubMed] [Google Scholar]
  15. Kopka M. L., Yoon C., Goodsell D., Pjura P., Dickerson R. E. The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc Natl Acad Sci U S A. 1985 Mar;82(5):1376–1380. doi: 10.1073/pnas.82.5.1376. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kumar K. A., Muniyappa K. Use of structure-directed DNA ligands to probe the binding of recA protein to narrow and wide grooves of DNA and on its ability to promote homologous pairing. J Biol Chem. 1992 Dec 5;267(34):24824–24832. [PubMed] [Google Scholar]
  17. Laundon C. H., Griffith J. D. Cationic metals promote sequence-directed DNA bending. Biochemistry. 1987 Jun 30;26(13):3759–3762. doi: 10.1021/bi00387a003. [DOI] [PubMed] [Google Scholar]
  18. Murialdo H. Bacteriophage lambda DNA maturation and packaging. Annu Rev Biochem. 1991;60:125–153. doi: 10.1146/annurev.bi.60.070191.001013. [DOI] [PubMed] [Google Scholar]
  19. Schmid N., Behr J. P. Location of spermine and other polyamines on DNA as revealed by photoaffinity cleavage with polyaminobenzenediazonium salts. Biochemistry. 1991 Apr 30;30(17):4357–4361. doi: 10.1021/bi00231a035. [DOI] [PubMed] [Google Scholar]
  20. Straney D. C., Crothers D. M. Effect of drug-DNA interactions upon transcription initiation at the lac promoter. Biochemistry. 1987 Apr 7;26(7):1987–1995. doi: 10.1021/bi00381a031. [DOI] [PubMed] [Google Scholar]
  21. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. doi: 10.1038/308509a0. [DOI] [PubMed] [Google Scholar]
  22. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  23. Zimmer C., Wähnert U. Nonintercalating DNA-binding ligands: specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material. Prog Biophys Mol Biol. 1986;47(1):31–112. doi: 10.1016/0079-6107(86)90005-2. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES