Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1988 Nov 25;16(22):10733–10750. doi: 10.1093/nar/16.22.10733

Effects of palindromes on in vivo DNA replication and mutagenesis in bacteriophage phi X174 RF DNA.

U R Müller 1, B K Perkins 1, W L Williams 1
PMCID: PMC338936  PMID: 2974537

Abstract

Bacteriophage phi X174 mutants with insertions of palindromic DNA sequences are rapidly outgrown by competing wild-type phage (Müller & Turnage, J. Mol. Biol. 189: 285). The basis for this defect was investigated and found to be due to an exclusion event early in the infectious cycle, in which phage genomes with palindromic inserts were preferentially excluded by wt phage. In addition, we have obtained further evidence for a palindrome induced genetic instability. Both defects are dependent on palindrome size and sequence, consistent with a model which involves formation of cruciforms, or cruciform-like structures. We propose that formation of unusual DNA secondary structures reduces the effectiveness of replicative form (RF) DNA to interact with limiting replication factors or membrane binding sites, possibly because of interaction with the host recombination system.

Full text

PDF
10733

Images in this article

10738Image
on p.10738
10740Image
on p.10740

Selected References

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

  1. Borrias W. E., van de Pol J. H., van de Vate C., van Arkel G. A. Complementation experiments between conditional lethal mutants of bacteriophage psiX 174. Mol Gen Genet. 1969 Oct 13;105(2):152–163. doi: 10.1007/BF00445685. [DOI] [PubMed] [Google Scholar]
  2. Collins J. Instability of palindromic DNA in Escherichia coli. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 1):409–416. doi: 10.1101/sqb.1981.045.01.055. [DOI] [PubMed] [Google Scholar]
  3. Collins J., Volckaert G., Nevers P. Precise and nearly-precise excision of the symmetrical inverted repeats of Tn5; common features of recA-independent deletion events in Escherichia coli. Gene. 1982 Jul-Aug;19(1):139–146. doi: 10.1016/0378-1119(82)90198-6. [DOI] [PubMed] [Google Scholar]
  4. Hayashi M. N., Hayashi M., Müller U. R. Role for the J-F intercistronic region of bacteriophages phi X174 and G4 in stability of mRNA. J Virol. 1983 Oct;48(1):186–196. doi: 10.1128/jvi.48.1.186-196.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hsu M. T. Electron microscopic evidence for the cruciform structure in intracellular SV40 DNA. Virology. 1985 Jun;143(2):617–621. doi: 10.1016/0042-6822(85)90400-3. [DOI] [PubMed] [Google Scholar]
  6. Incardona N. L., Müller U. R. Eclipse kinetics as a probe of quaternary structure in bacteriophage phi X174. J Mol Biol. 1985 Feb 20;181(4):479–486. doi: 10.1016/0022-2836(85)90421-8. [DOI] [PubMed] [Google Scholar]
  7. Jaworski A., Hsieh W. T., Blaho J. A., Larson J. E., Wells R. D. Left-handed DNA in vivo. Science. 1987 Nov 6;238(4828):773–777. doi: 10.1126/science.3313728. [DOI] [PubMed] [Google Scholar]
  8. Leach D. R., Stahl F. W. Viability of lambda phages carrying a perfect palindrome in the absence of recombination nucleases. 1983 Sep 29-Oct 5Nature. 305(5933):448–451. doi: 10.1038/305448a0. [DOI] [PubMed] [Google Scholar]
  9. Lilley D. M., Kemper B. Cruciform-resolvase interactions in supercoiled DNA. Cell. 1984 Feb;36(2):413–422. doi: 10.1016/0092-8674(84)90234-4. [DOI] [PubMed] [Google Scholar]
  10. Mizuuchi K., Kemper B., Hays J., Weisberg R. A. T4 endonuclease VII cleaves holliday structures. Cell. 1982 Jun;29(2):357–365. doi: 10.1016/0092-8674(82)90152-0. [DOI] [PubMed] [Google Scholar]
  11. Müller U. R. Enzymatic construction and selection of bacteriophage G4 mutants with modifications of a DNA secondary structure in the J-F intercistronic region. J Virol. 1983 Oct;48(1):170–179. doi: 10.1128/jvi.48.1.170-179.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Müller U. R., Turnage M. A. Insertions of palindromic DNA sequences into the J-F intercistronic region of bacteriophage phi X174 interfere with normal phage growth. J Mol Biol. 1986 May 20;189(2):285–292. doi: 10.1016/0022-2836(86)90510-3. [DOI] [PubMed] [Google Scholar]
  13. Müller U. R., Wells R. D. Intercistronic regions in phi X174 DNA. I. Construction of mutants with altered intercistronic regions between genes J and F. J Mol Biol. 1980 Jul 25;141(1):1–24. doi: 10.1016/s0022-2836(80)80026-x. [DOI] [PubMed] [Google Scholar]
  14. Müller U. R., Wells R. D. Intercistronic regions in phi X174 DNA. II. Biochemical and biological analysis of mutants with altered intercistronic regions between genes J and F. J Mol Biol. 1980 Jul 25;141(1):25–41. doi: 10.1016/s0022-2836(80)80027-1. [DOI] [PubMed] [Google Scholar]
  15. Müller U. R., Wilson C. L. The effect of supercoil and temperature on the recognition of palindromic and non-palindromic regions in phi X174 replicative form DNA by S1 and Bal31. J Biol Chem. 1987 Mar 15;262(8):3730–3738. [PubMed] [Google Scholar]
  16. Panayotatos N., Fontaine A. A native cruciform DNA structure probed in bacteria by recombinant T7 endonuclease. J Biol Chem. 1987 Aug 15;262(23):11364–11368. [PubMed] [Google Scholar]
  17. Romantschuk M. L., Müller U. R. Mutations in the J-F intercistronic region of bacteriophages phi X174 and G4 affect the regulation of gene expression. J Virol. 1983 Oct;48(1):180–185. doi: 10.1128/jvi.48.1.180-185.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Russell P. W., Müller U. R. Construction of bacteriophage luminal diameterX174 mutants with maximum genome sizes. J Virol. 1984 Dec;52(3):822–827. doi: 10.1128/jvi.52.3.822-827.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Salivar W. O., Sinsheimer R. L. Intracellular location and number of replicating parental DNA molecules of bacteriophages lambda and phi-X174. J Mol Biol. 1969 Apr 14;41(1):39–65. doi: 10.1016/0022-2836(69)90124-7. [DOI] [PubMed] [Google Scholar]
  20. Sanger F., Coulson A. R., Friedmann T., Air G. M., Barrell B. G., Brown N. L., Fiddes J. C., Hutchison C. A., 3rd, Slocombe P. M., Smith M. The nucleotide sequence of bacteriophage phiX174. J Mol Biol. 1978 Oct 25;125(2):225–246. doi: 10.1016/0022-2836(78)90346-7. [DOI] [PubMed] [Google Scholar]
  21. Warren G. J., Green R. L. Comparison of physical and genetic properties of palindromic DNA sequences. J Bacteriol. 1985 Mar;161(3):1103–1111. doi: 10.1128/jb.161.3.1103-1111.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Williams W. L., Müller U. R. Effects of palindrome size and sequence on genetic stability in the bacteriophage phi X174 genome. J Mol Biol. 1987 Aug 20;196(4):743–755. doi: 10.1016/0022-2836(87)90401-3. [DOI] [PubMed] [Google Scholar]

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

RESOURCES