In vitro selection of integration host factor binding sites

Journal of Bacteriology

Volumn 181, Issue 10, 1999, Pages 3246-3255

  Goodman, Steven D ^a   Velten, Nerissa J ^a   Gao, Qian ^a   Robinson, Scott ^b   Segall, Anca M ^b  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRATION HOST FACTOR;

AMINO ACID SEQUENCE; ARTICLE; BACTERIOPHAGE LAMBDA; BACTERIUM; BASE PAIRING; BINDING AFFINITY; BINDING SITE; DNA ADDUCT; DNA FLANKING REGION; DNA FOOTPRINTING; DNA SEQUENCE; GENETIC RECOMBINATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION;

BACTERIA (MICROORGANISMS); BACTERIOPHAGE LAMBDA; PROKARYOTA;

EID: 0032934143     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.181.10.3246-3255.1999     Document Type: Article

References (40)

1. Betermier, M., D. J. Galas, and M. Chandler. 1994. Interactions of Fis protein with DNA: bending and specificity. Biochimie 76:958-967.
2. Craig, N. L., and H. A. Nash. 1984. E. coli integration host factor binds to specific sites in DNA. Cell 39:707-716.
3. Cui, Y., Q. Wang, G. D. Stormo, and J. M. Calvo. 1995. A consensus sequence for binding of LRP to DNA. J. Bacteriol. 177:4872-4880.
4. Gardner, J. F., and H. A. Nash. 1986. Role of Escherichia coli IHF protein in lambda site-specific recombination: a mutational analysis of binding sites. J. Mol. Biol. 191:181-189.
5. Goodman, S. D., and H. A. Nash. 1989. Functional replacement of a protein-induced bend in a DNA recombination site. Nature 341:251-254.
6. Goodman, S. D., S. C. Nicholson, and H. A. Nash. 1992. Deformation of DNA during site-specific recombination of bacteriophage X: replacement of IHF protein by HU protein or sequence-directed bends. Proc. Natl. Acad. Sci. USA 89:11910-11914.
7. Goodrich, J. A., M. L. Schwartz, and W. R. McClure. 1990. 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. 18:4993-5000.
8. Hagerman, P. J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:265-286.
9. Hales, L. M., R. I. Gumport, and J. F. Gardner. 1994. Determining the DNA sequence elements required for binding integration host factor to two different target sites. J. Bacteriol. 176:2999-3006.
10. Hales, L. M., R. I. Gumport, and J. F. Gardner. 1994. Mutants of Escherichia coli integration host factor: DNA-binding and recombination properties. Biochimie 76:1030-1040.
11. Hales, L. M., R. I. Gumport, and J. F. Gardner. 1996. Examining the contribution of a dA+dT element to the conformation of Escherichia coli integration host factor-DNA complexes. Nucleic Acids Res. 24:1780-1786.
12. Hengen, P. N., S. L. Bartram, L. E. Stewart, and T. D. Schneider. 1997. Information analysis of Fis binding sites. Nucleic Acids Res. 25:4994-5002.
13. Irvine, D., C. Tuerk, and L. Gold. 1991. SELEXION, systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis. J. Mol. Biol. 222:739-761.
14. Kim, S., and A. Landy. 1992. Lambda Int protein bridges between higher order complexes at two distant chromosomal loci attL and atlR. Science 256: 198-203.
15. Kim, S., L. Moitoso de Vargas, S. E. Nunes-Duby, and A. Landy. 1990. Mapping of a higher order protein-DNA complex: two kinds of long-range interactions in λ attL. Cell 63:773-781.
16. Lee, E. C., M. P. MacWilliams, R. I. Gumport, and J. F. Gardner. 1991. Genetic analysis of Escherichia coli integration host factor interactions with its bacteriophage λ H′ recognition site. J. Bacteriol. 173:609-617.
17. Lee, E. C., L. M. Hales, R. I. Gumport, and J. F. Gardner. 1992. The isolation and characterization of mutants of the integration host factor (IHF) of Escherichia coli with altered, expanded DNA-binding specificities. EMBO J. 11:305-313.
18. MacWilliams, M., R. I. Gumport, and J. F. Gardner. 1997. Mutational analysis of protein binding sites involved in formation of the bacteriophage λ attL complex. J. Bacteriol. 179:1059-1067.
19. Nash, H. A. 1996. The HU and IHF proteins: accessory factors for complex protein-DNA assemblies, p. 149-179. In E. C. C. Lin and A. S. Lynch (ed.), Regulation of gene expression in Escherichia coli. R. G. Landes Co., Austin. Tex.
20. Numrych, T. E., R. I. Gumport, and J. F. Gardner. 1990. 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. 18:3953-3959.
21. Nunes-Duby, S. E., L. I. Smith-Mungo, and A. Landy. 1995. Single base-pair precision and structural rigidity in a small IMF-induced DNA loop. J. Mol. Biol. 253:228-242.
22. Oberto, J., K. Drlica, and J. Rouviere-Yaniv. 1994. Histones, HMG, HU, IMF: meme combat. Biochimie 76:901-908.
23. Peacock, S., H. Weissbach, and H. A. Nash. 1984. In vitro regulation of phage λ cII gene expression by Escherichia coli integration host factor. Proc. Natl. Acad. Sci. USA 81:6009-6013.
24. Rice, P. A., S. Yang, K. Mizuuchi, and H. A. Nash. 1996. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-tum. Cell 87:1295-1306.
25. Rice, P. A. 1997. Making DNA do a U-turn: IHF and related proteins. Curr. Opin. Struct. Biol. 7:86-93.
26. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
27. Segall, A. M., S. D. Goodman, and H. A. Nash. 1994. Architectural elements in nucleoprotein complexes: interchangeability of specific and non-specific DNA binding proteins. EMBO J. 13:4536-4548.
28. Shindo, H., F. Kanke, M. Miyake, U. Matsumoto, and M. Shimizu. 1995. 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. 18:1328-1334.
29. Spurio, R., M. Falconi, A. Brandi, C. L. Pon, and C. O. Gualerzi. 1997. The oligomeric structure of nucleoid protein H-NS is necessary for recognition of intrinsically curved DNA and for DNA bending. EMBO J. 16:1795-1805.
30. Strauss, J. K., and L. J. Maher. 1994. DNA bending by asymmetric phosphate neutralization. Science 266:1829-1833.
31. 4 and by DNA cyclization studies. Biochemistry 35:10815-10827.
32. Tuerk, C., and L. Gold. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510.
33. Vant-Hull, B., A. Payano-Baez, R. H. Davis, and L. Gold. 1998. The mathematics of SELEX against complex targets. J. Mol. Biol. 278:579-597.
34. von Hippel, P. H. 1994. Protein-DNA recognition: new perspectives and underlying themes. Science 263:769-770.
35. Werner, M. H., G. M. Clore, A. M. Gronenborn, and H. A. Nash. 1994. Symmetry and asymmetry in the function of Escherichia coli integration host factor: implications for target identification by DNA-binding proteins. Curr. Biol. 4:477-487.
36. Williams, J. G. K., D. L. Wulf, and H. A. Nash. 1977. A mutant of Escherichia coli deficient in a host function required for phage lambda integration and excision, p. 357-361. In A. Bukhari, J. Shapiro, and S. Adhya (ed.), DNA insertion elements, plasmids and episomes. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
37. Yamada, H., S. Muramatsu, and T. Mizuno. 1990. An Escherichia coli protein that preferentially binds to sharply curved DNA. J. Biochem. 108:420-425.
38. Yang, C.-C., and H. A. Nash. 1989. The interaction of E. coli IHF protein with its specific binding sites. Cell 57:869-880.
39. Yang, S.-W., and H. A. Nash. 1994. Specific photocrosslinking of DNA-protein complexes: identification of contacts between integration host factor and its DNA target. Proc. Natl. Acad. Sci. USA 91:12183-12187.
40. Yang, S.-W., and H. A. Nash. 1995. Comparison of protein binding to DNA in vivo and in vitro: defining an effective intracellular target. EMBO J. 14:6292-6300.