Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1994 Mar;176(5):1364–1373. doi: 10.1128/jb.176.5.1364-1373.1994

Determinants of affinity and mode of DNA binding at the carboxy terminus of the bacteriophage SPO1-encoded type II DNA-binding protein, TF1.

L Andera 1, E P Geiduschek 1
PMCID: PMC205201  PMID: 8113176

Abstract

The role of the carboxy-terminal amino acids of the bacteriophage SPO1-encoded type II DNA-binding protein, TF1, in DNA binding was analyzed. Chain-terminating mutations truncating the normally 99-amino-acid TF1 at amino acids 96, 97, and 98 were constructed, as were missense mutations substituting cysteine, arginine, and serine for phenylalanine at amino acid 97 and tryptophan for lysine at amino acid 99. The binding of the resulting proteins to a synthetic 44-bp binding site in 5-(hydroxymethyl)uracil DNA, to binding sites in larger SPO1 [5-(hydroxymethyl)uracil-containing] DNA fragments, and to thymine-containing homologous DNA was analyzed by gel retardation and also by DNase I and hydroxy radical footprinting. We conclude that the C tail up to and including phenylalanine at amino acid 97 is essential for DNA binding and that the two C-terminal amino acids, 98 and 99, are involved in protein-protein interactions between TF1 dimers bound to DNA.

Full text

PDF
1364

Images in this article

1367Image
on p.1367
1368Image
on p.1368
1369Image
on p.1369
1370Image
on p.1370
1371Image
on p.1371
1371Image
on p.1371

Selected References

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

  1. Boubrik F., Bonnefoy E., Rouvière-Yaniv J. HU and IHF: similarities and differences. In Escherichia coli, the lack of HU is not compensated for by IHF. Res Microbiol. 1991 Feb-Apr;142(2-3):239–247. doi: 10.1016/0923-2508(91)90036-a. [DOI] [PubMed] [Google Scholar]
  2. Craig N. L., Nash H. A. E. coli integration host factor binds to specific sites in DNA. Cell. 1984 Dec;39(3 Pt 2):707–716. doi: 10.1016/0092-8674(84)90478-1. [DOI] [PubMed] [Google Scholar]
  3. Freundlich M., Ramani N., Mathew E., Sirko A., Tsui P. The role of integration host factor in gene expression in Escherichia coli. Mol Microbiol. 1992 Sep;6(18):2557–2563. doi: 10.1111/j.1365-2958.1992.tb01432.x. [DOI] [PubMed] [Google Scholar]
  4. Friedman D. I. Integration host factor: a protein for all reasons. Cell. 1988 Nov 18;55(4):545–554. doi: 10.1016/0092-8674(88)90213-9. [DOI] [PubMed] [Google Scholar]
  5. Gardner J. F., Nash H. A. Role of Escherichia coli IHF protein in lambda site-specific recombination. A mutational analysis of binding sites. J Mol Biol. 1986 Sep 20;191(2):181–189. doi: 10.1016/0022-2836(86)90255-x. [DOI] [PubMed] [Google Scholar]
  6. Granston A. E., Nash H. A. Characterization of a set of integration host factor mutants deficient for DNA binding. J Mol Biol. 1993 Nov 5;234(1):45–59. doi: 10.1006/jmbi.1993.1562. [DOI] [PubMed] [Google Scholar]
  7. Greene J. R., Geiduschek E. P. Site-specific DNA binding by the bacteriophage SP01-encoded type II DNA-binding protein. EMBO J. 1985 May;4(5):1345–1349. doi: 10.1002/j.1460-2075.1985.tb03783.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hoover T. R., Santero E., Porter S., Kustu S. The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons. Cell. 1990 Oct 5;63(1):11–22. doi: 10.1016/0092-8674(90)90284-l. [DOI] [PubMed] [Google Scholar]
  9. Huisman O., Faelen M., Girard D., Jaffé A., Toussaint A., Rouvière-Yaniv J. Multiple defects in Escherichia coli mutants lacking HU protein. J Bacteriol. 1989 Jul;171(7):3704–3712. doi: 10.1128/jb.171.7.3704-3712.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Härd T., Hsu V., Sayre M. H., Geiduschek E. P., Appelt K., Kearns D. R. Fluorescence studies of a single tyrosine in a type II DNA binding protein. Biochemistry. 1989 Jan 10;28(1):396–406. doi: 10.1021/bi00427a055. [DOI] [PubMed] [Google Scholar]
  11. Johnson G. G., Geiduschek E. P. Specificity of the weak binding between the phage SPO1 transcription-inhibitory protein, TF1, and SPO1 DNA. Biochemistry. 1977 Apr 5;16(7):1473–1485. doi: 10.1021/bi00626a036. [DOI] [PubMed] [Google Scholar]
  12. Kano Y., Imamoto F. Requirement of integration host factor (IHF) for growth of Escherichia coli deficient in HU protein. Gene. 1990 Apr 30;89(1):133–137. doi: 10.1016/0378-1119(90)90216-e. [DOI] [PubMed] [Google Scholar]
  13. Kano Y., Ogawa T., Ogura T., Hiraga S., Okazaki T., Imamoto F. Participation of the histone-like protein HU and of IHF in minichromosomal maintenance in Escherichia coli. Gene. 1991 Jul 15;103(1):25–30. doi: 10.1016/0378-1119(91)90386-p. [DOI] [PubMed] [Google Scholar]
  14. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  15. Mengeritsky G., Goldenberg D., Mendelson I., Giladi H., Oppenheim A. B. Genetic and biochemical analysis of the integration host factor of Escherichia coli. J Mol Biol. 1993 Jun 5;231(3):646–657. doi: 10.1006/jmbi.1993.1316. [DOI] [PubMed] [Google Scholar]
  16. Mensa-Wilmot K., Carroll K., McMacken R. Transcriptional activation of bacteriophage lambda DNA replication in vitro: regulatory role of histone-like protein HU of Escherichia coli. EMBO J. 1989 Aug;8(8):2393–2402. doi: 10.1002/j.1460-2075.1989.tb08369.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Neilan J. G., Lu Z., Kutish G. F., Sussman M. D., Roberts P. C., Yozawa T., Rock D. L. An African swine fever virus gene with similarity to bacterial DNA binding proteins, bacterial integration host factors, and the Bacillus phage SPO1 transcription factor, TF1. Nucleic Acids Res. 1993 Mar 25;21(6):1496–1496. doi: 10.1093/nar/21.6.1496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Ogura T., Niki H., Kano Y., Imamoto F., Hiraga S. Maintenance of plasmids in HU and IHF mutants of Escherichia coli. Mol Gen Genet. 1990 Jan;220(2):197–203. doi: 10.1007/BF00260482. [DOI] [PubMed] [Google Scholar]
  19. Pendergrast P. S., Chen Y., Ebright Y. W., Ebright R. H. Determination of the orientation of a DNA binding motif in a protein-DNA complex by photocrosslinking. Proc Natl Acad Sci U S A. 1992 Nov 1;89(21):10287–10291. doi: 10.1073/pnas.89.21.10287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Reisman J. M., Hsu V. L., Jariel-Encontre I., Lecou C., Sayre M. H., Kearns D. R., Parello J. A 1H-NMR study of the transcription factor 1 from Bacillus subtilis phage SPO1 by selective 2H-labeling. Complete assignment and structural analysis of the aromatic resonances for a 22-kDa homodimer. Eur J Biochem. 1993 Apr 15;213(2):865–873. doi: 10.1111/j.1432-1033.1993.tb17830.x. [DOI] [PubMed] [Google Scholar]
  21. Robertson C. A., Nash H. A. Bending of the bacteriophage lambda attachment site by Escherichia coli integration host factor. J Biol Chem. 1988 Mar 15;263(8):3554–3557. [PubMed] [Google Scholar]
  22. Sayre M. H., Geiduschek E. P. Construction and properties of a temperature-sensitive mutation in the gene for the bacteriophage SPO1 DNA-binding protein TF1. J Bacteriol. 1990 Aug;172(8):4672–4681. doi: 10.1128/jb.172.8.4672-4681.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Sayre M. H., Geiduschek E. P. Effects of mutations at amino acid 61 in the arm of TF1 on its DNA-binding properties. J Mol Biol. 1990 Dec 20;216(4):819–833. doi: 10.1016/S0022-2836(99)80004-7. [DOI] [PubMed] [Google Scholar]
  24. Sayre M. H., Geiduschek E. P. TF1, the bacteriophage SPO1-encoded type II DNA-binding protein, is essential for viral multiplication. J Virol. 1988 Sep;62(9):3455–3462. doi: 10.1128/jvi.62.9.3455-3462.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Schmid M. B., Johnson R. C. Southern revival--news of bacterial chromatin. Prokaryotic chromosomes: structure and function in genome design. Fifth Annual University of Alabama at Birmingham Biochemistry symposium, Panama City, FL, USA, May 8-12, 1991. New Biol. 1991 Oct;3(10):945–950. [PubMed] [Google Scholar]
  26. Schneider G. J., Geiduschek E. P. Stoichiometry of DNA binding by the bacteriophage SP01-encoded type II DNA-binding protein TF1. J Biol Chem. 1990 Jun 25;265(18):10198–10200. [PubMed] [Google Scholar]
  27. Schneider G. J., Sayre M. H., Geiduschek E. P. DNA-bending properties of TF1. J Mol Biol. 1991 Oct 5;221(3):777–794. doi: 10.1016/0022-2836(91)80175-t. [DOI] [PubMed] [Google Scholar]
  28. Smith B. D., Nakanishi K., Watanabe K., Ito S. 4-Azido[3,5-3H]phenacyl bromide, a versatile bifunctional reagent for photoaffinity radiolabeling. Synthesis of prostaglandin 4-azido[3,5-3H]phenacyl esters. Bioconjug Chem. 1990 Sep-Oct;1(5):363–364. doi: 10.1021/bc00005a011. [DOI] [PubMed] [Google Scholar]
  29. Tanaka I., Appelt K., Dijk J., White S. W., Wilson K. S. 3-A resolution structure of a protein with histone-like properties in prokaryotes. Nature. 1984 Aug 2;310(5976):376–381. doi: 10.1038/310376a0. [DOI] [PubMed] [Google Scholar]
  30. White S. W., Appelt K., Wilson K. S., Tanaka I. A protein structural motif that bends DNA. Proteins. 1989;5(4):281–288. doi: 10.1002/prot.340050405. [DOI] [PubMed] [Google Scholar]
  31. Wilson D. L., Geiduschek E. P. A template-selective inhibitor of in vitro transcription. Proc Natl Acad Sci U S A. 1969 Feb;62(2):514–520. doi: 10.1073/pnas.62.2.514. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Yang C. C., Nash H. A. The interaction of E. coli IHF protein with its specific binding sites. Cell. 1989 Jun 2;57(5):869–880. doi: 10.1016/0092-8674(89)90801-5. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES