In Vitro Selection of Integration Host Factor Binding Sites
10.1128/jb.181.10.3246-3255.1999
Crossref journal-article
American Society for Microbiology
Journal of Bacteriology (235)
Abstract

ABSTRACT Integration host factor (IHF) is a bacterial protein that binds and severely bends a specific DNA target. IHF binding sites are approximately 30 to 35 bp long and are apparently divided into two domains. While the 3′ domain is conserved, the 5′ domain is degenerate but is typically AT rich. As a result of physical constraints that IHF must impose on DNA in order to bind, it is believed that this 5′ domain must possess structural characteristics conducive for both binding and bending with little regard for specific contacts between the protein and the DNA. We have examined the sequence requirements of the 5′ binding domain of the IHF binding target. Using a SELEX procedure, we randomized and selected variants of a natural IHF site. We then analyzed these variants to determine how the 5′ binding domain affects the structure, affinity, and function of an IHF-DNA complex in a native system. Despite finding individual sequences that varied over 100-fold in affinity for IHF, we found no apparent correlation between affinity and function.

Bibliography

Goodman, S. D., Velten, N. J., Gao, Q., Robinson, S., & Segall, A. M. (1999). In Vitro Selection of Integration Host Factor Binding Sites. Journal of Bacteriology, 181(10), 3246–3255.

Authors 5
  1. Steven D. Goodman (first)
  2. Nerissa J. Velten (additional)
  3. Qian Gao (additional)
  4. Scott Robinson (additional)
  5. Anca M. Segall (additional)
References 40 Referenced 48
  1. Betermier M. Galas D. J. Chandler M. Interactions of Fis protein with DNA: bending and specificity.Biochimie761994958967 (10.1016/0300-9084(94)90021-3) / Biochimie / Interactions of Fis protein with DNA: bending and specificity by Betermier M. (1994)
  2. Craig N. L. Nash H. A. E. coli integration host factor binds to specific sites in DNA.Cell391984707716 (10.1016/0092-8674(84)90478-1) / Cell / E. coli integration host factor binds to specific sites in DNA by Craig N. L. (1984)
  3. 10.1128/jb.177.17.4872-4880.1995
  4. 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.1911986181189 (10.1016/0022-2836(86)90255-X) / J. Mol. Biol. / Role of Escherichia coli IHF protein in lambda site-specific recombination: a mutational analysis of binding sites by Gardner J. F. (1986)
  5. Goodman S. D. Nash H. A. Functional replacement of a protein-induced bend in a DNA recombination site.Nature3411989251254 (10.1038/341251a0) / Nature / Functional replacement of a protein-induced bend in a DNA recombination site by Goodman S. D. (1989)
  6. Goodman S. D. Nicholson S. C. Nash H. A. Deformation of DNA during site-specific recombination of bacteriophage λ: replacement of IHF protein by HU protein or sequence-directed bends.Proc. Natl. Acad. Sci. USA8919921191011914 (10.1073/pnas.89.24.11910) / Proc. Natl. Acad. Sci. USA / Deformation of DNA during site-specific recombination of bacteriophage λ: replacement of IHF protein by HU protein or sequence-directed bends by Goodman S. D. (1992)
  7. Goodrich J. A. Schwartz M. L. McClure W. R. Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF).Nucleic Acids Res.18199049935000 (10.1093/nar/18.17.4993) / Nucleic Acids Res. / Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF) by Goodrich J. A. (1990)
  8. Hagerman P. J. Flexibility of DNA.Annu. Rev. Biophys. Biophys. Chem.171988265286 (10.1146/annurev.bb.17.060188.001405) / Annu. Rev. Biophys. Biophys. Chem. / Flexibility of DNA by Hagerman P. J. (1988)
  9. 10.1128/jb.176.10.2999-3006.1994
  10. Hales L. M. Gumport R. I. Gardner J. F. Mutants of Escherichia coli integration host factor: DNA-binding and recombination properties.Biochimie76199410301040 (10.1016/0300-9084(94)90027-2) / Biochimie / Mutants of Escherichia coli integration host factor: DNA-binding and recombination properties by Hales L. M. (1994)
  11. Hales L. M. Gumport R. I. Gardner J. F. Examining the contribution of a dA+dT element to the conformation of Escherichia coli integration host factor-DNA complexes.Nucleic Acids Res.24199617801786 (10.1093/nar/24.9.1780) / Nucleic Acids Res. / Examining the contribution of a dA+dT element to the conformation of Escherichia coli integration host factor-DNA complexes by Hales L. M. (1996)
  12. Hengen P. N. Bartram S. L. Stewart L. E. Schneider T. D. Information analysis of Fis binding sites.Nucleic Acids Res.25199749945002 (10.1093/nar/25.24.4994) / Nucleic Acids Res. / Information analysis of Fis binding sites by Hengen P. N. (1997)
  13. Irvine D. Tuerk C. Gold L. SELEXION, systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis.J. Mol. Biol.2221991739761 / J. Mol. Biol. / SELEXION, systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis by Irvine D. (1991)
  14. Kim S. Landy A. Lambda Int protein bridges between higher order complexes at two distant chromosomal loci attL and attR.Science2561992198203 (10.1126/science.1533056) / Science / Lambda Int protein bridges between higher order complexes at two distant chromosomal loci attL and attR by Kim S. (1992)
  15. Kim S. Moitoso de Vargas L. Nunes-Duby S. E. Landy A. Mapping of a higher order protein-DNA complex: two kinds of long-range interactions in λ attL.Cell631990773781 (10.1016/0092-8674(90)90143-3) / Cell / Mapping of a higher order protein-DNA complex: two kinds of long-range interactions in λ attL by Kim S. (1990)
  16. 10.1128/jb.173.2.609-617.1991
  17. Lee E. C. Hales L. M. Gumport R. I. Gardner J. F. The isolation and characterization of mutants of the integration host factor (IHF) of Escherichia coli with altered, expanded DNA-binding specificities.EMBO J.111992305313 (10.1002/j.1460-2075.1992.tb05053.x) / EMBO J. / The isolation and characterization of mutants of the integration host factor (IHF) of Escherichia coli with altered, expanded DNA-binding specificities by Lee E. C. (1992)
  18. 10.1128/jb.179.4.1059-1067.1997
  19. Nash H. A. The HU and IHF proteins: accessory factors for complex protein-DNA assemblies Regulation of gene expression in Escherichia coli. R. G. Lin E. C. C. Lynch A. S. 1996 149 179 Landes Co. Austin Tex (10.1007/978-1-4684-8601-8_8)
  20. Numrych T. E. Gumport R. I. Gardner J. F. A comparison of the effects of single-base and triple-base changes in the integrase arm-type binding sites on the site-specific recombination of bacteriophage lambda.Nucleic Acids Res.18199039533959 (10.1093/nar/18.13.3953) / Nucleic Acids Res. / A comparison of the effects of single-base and triple-base changes in the integrase arm-type binding sites on the site-specific recombination of bacteriophage lambda by Numrych T. E. (1990)
  21. Nunes-Duby S. E. Smith-Mungo L. I. Landy A. Single base-pair precision and structural rigidity in a small IHF-induced DNA loop.J. Mol. Biol.2531995228242 (10.1006/jmbi.1995.0548) / J. Mol. Biol. / Single base-pair precision and structural rigidity in a small IHF-induced DNA loop by Nunes-Duby S. E. (1995)
  22. Oberto J. Drlica K. Rouviere-Yaniv J. Histones, HMG, HU, IHF: meme combat.Biochimie761994901908 (10.1016/0300-9084(94)90014-0) / Biochimie / Histones, HMG, HU, IHF: meme combat by Oberto J. (1994)
  23. Peacock S. Weissbach H. Nash H. A. In vitro regulation of phage λ c II gene expression by Escherichia coli integration host factor.Proc. Natl. Acad. Sci. USA81198460096013 (10.1073/pnas.81.19.6009) / Proc. Natl. Acad. Sci. USA / In vitro regulation of phage λ c II gene expression by Escherichia coli integration host factor by Peacock S. (1984)
  24. Rice P. A. Yang S. Mizuuchi K. Nash H. A. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn.Cell87199612951306 (10.1016/S0092-8674(00)81824-3) / Cell / Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn by Rice P. A. (1996)
  25. Rice P. A. Making DNA do a U-turn: IHF and related proteins.Curr. Opin. Struct. Biol.719978693 (10.1016/S0959-440X(97)80011-5) / Curr. Opin. Struct. Biol. / Making DNA do a U-turn: IHF and related proteins by Rice P. A. (1997)
  26. Sambrook J. Fritsch E. F. Maniatis T. Molecular cloning: a laboratory manual 2nd ed. 1989 Cold Spring Harbor Laboratory Press Cold Spring Harbor N.Y
  27. Segall A. M. Goodman S. D. Nash H. A. Architectural elements in nucleoprotein complexes: interchangeability of specific and non-specific DNA binding proteins.EMBO J.13199445364548 (10.1002/j.1460-2075.1994.tb06775.x) / EMBO J. / Architectural elements in nucleoprotein complexes: interchangeability of specific and non-specific DNA binding proteins by Segall A. M. (1994)
  28. Shindo H. Kanke F. Miyake M. Matsumoto U. Shimizu M. The binding specificity and affinity of E. coli integration host factor (IHF) are influenced by the flexibility of flanking regions of its recognition sites.Biol. Pharm. Bull.18199513281334 (10.1248/bpb.18.1328) / Biol. Pharm. Bull. / The binding specificity and affinity of E. coli integration host factor (IHF) are influenced by the flexibility of flanking regions of its recognition sites by Shindo H. (1995)
  29. Spurio R. Falconi M. Brandi A. Pon C. L. Gualerzi C. O. The oligomeric structure of nucleoid protein H-NS is necessary for recognition of intrinsically curved DNA and for DNA bending.EMBO J.16199717951805 (10.1093/emboj/16.7.1795) / EMBO J. / The oligomeric structure of nucleoid protein H-NS is necessary for recognition of intrinsically curved DNA and for DNA bending by Spurio R. (1997)
  30. Strauss J. K. Maher L. J. DNA bending by asymmetric phosphate neutralization.Science266199418291833 (10.1126/science.7997878) / Science / DNA bending by asymmetric phosphate neutralization by Strauss J. K. (1994)
  31. Sun D. Hurley L. H. Harshey R. M. Structural distortions induced by integration host factor (IHF) at the H′ site of phage λ probed by (+)-CC-1065, pluramycin, and KMnO4 and by DNA cyclization studies.Biochemistry3519961081510827 (10.1021/bi952786x) / Biochemistry / Structural distortions induced by integration host factor (IHF) at the H′ site of phage λ probed by (+)-CC-1065, pluramycin, and KMnO4 and by DNA cyclization studies by Sun D. (1996)
  32. 10.1126/science.2200121
  33. Vant-Hull B. Payano-Baez A. Davis R. H. Gold L. The mathematics of SELEX against complex targets.J. Mol. Biol.2781998579597 (10.1006/jmbi.1998.1727) / J. Mol. Biol. / The mathematics of SELEX against complex targets by Vant-Hull B. (1998)
  34. von Hippel P. H. Protein-DNA recognition: new perspectives and underlying themes.Science2631994769770 (10.1126/science.8303292) / Science / Protein-DNA recognition: new perspectives and underlying themes by von Hippel P. H. (1994)
  35. Werner M. H. Clore G. M. Gronenborn A. M. Nash H. A. Symmetry and asymmetry in the function of Escherichia coli integration host factor: implications for target identification by DNA-binding proteins.Curr. Biol.41994477487 (10.1016/S0960-9822(00)00108-1) / Curr. Biol. / Symmetry and asymmetry in the function of Escherichia coli integration host factor: implications for target identification by DNA-binding proteins by Werner M. H. (1994)
  36. Williams J. G. K. Wulff D. L. Nash H. A. A mutant of Escherichia coli deficient in a host function required for phage lambda integration and excision DNA insertion elements plasmids and episomes. Bukhari A. Shapiro J. Adhya S. 1977 357 361 Cold Spring Harbor Laboratory Press Cold Spring Harbor N.Y
  37. Yamada H. Muramatsu S. Mizuno T. An Escherichia coli protein that preferentially binds to sharply curved DNA.J. Biochem.1081990420425 (10.1093/oxfordjournals.jbchem.a123216) / J. Biochem. / An Escherichia coli protein that preferentially binds to sharply curved DNA by Yamada H. (1990)
  38. Yang C.-C. Nash H. A. The interaction of E. coli IHF protein with its specific binding sites.Cell571989869880 (10.1016/0092-8674(89)90801-5) / Cell / The interaction of E. coli IHF protein with its specific binding sites by Yang C.-C. (1989)
  39. Yang S.-W. Nash H. A. Specific photocrosslinking of DNA-protein complexes: identification of contacts between integration host factor and its DNA target.Proc. Natl. Acad. Sci. USA9119941218312187 (10.1073/pnas.91.25.12183) / Proc. Natl. Acad. Sci. USA / Specific photocrosslinking of DNA-protein complexes: identification of contacts between integration host factor and its DNA target by Yang S.-W. (1994)
  40. Yang S.-W. Nash H. A. Comparison of protein binding to DNA in vivo and in vitro: defining an effective intracellular target.EMBO J.14199562926300 (10.1002/j.1460-2075.1995.tb00319.x) / EMBO J. / Comparison of protein binding to DNA in vivo and in vitro: defining an effective intracellular target by Yang S.-W. (1995)
Dates
Type When
Created 5 years, 7 months ago (Dec. 31, 2019, 11:34 a.m.)
Deposited 4 years ago (July 29, 2021, 1:46 p.m.)
Indexed 1 month, 1 week ago (July 16, 2025, 9:43 a.m.)
Issued 26 years, 3 months ago (May 15, 1999)
Published 26 years, 3 months ago (May 15, 1999)
Published Print 26 years, 3 months ago (May 15, 1999)
Funders 0

None

@article{Goodman_1999, title={In Vitro Selection of Integration Host Factor Binding Sites}, volume={181}, ISSN={1098-5530}, url={http://dx.doi.org/10.1128/jb.181.10.3246-3255.1999}, DOI={10.1128/jb.181.10.3246-3255.1999}, number={10}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Goodman, Steven D. and Velten, Nerissa J. and Gao, Qian and Robinson, Scott and Segall, Anca M.}, year={1999}, month=may, pages={3246–3255} }