Functional Characterization of the Escherichia coli Fis-DNA Binding Sequence

Journal of Molecular Biology

Volumn 376, Issue 3, 2008, Pages 771-785

  Shao, Yongping ^a   Feldman Cohen, Leah S ^b   Osuna, Robert ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

DNA bending; DNA binding; Fis; missing contact; nucleoid associated protein

Indexed keywords

FACTOR FOR INVERSION STIMULATION; THYMINE;

ARTICLE; BINDING AFFINITY; BINDING SITE; DNA BINDING; DNA SEQUENCE; DNA STRAND; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION;

ESCHERICHIA COLI;

EID: 38649140177     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.11.101     Document Type: Article

References (53)

1. Azam T.A., and Ishihama A. Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J. Biol. Chem. 274 (1999) 33105-33113
2. Boswell S., Mathew J., Beach M., Osuna R., and Colon W. Variable contributions of tyrosine residues to the structural and spectroscopic properties of the factor for inversion stimulation. Biochemistry 43 (2004) 2964-2977
3. Beach M.B., and Osuna R. Identification and characterization of the fis operon in enteric bacteria. J. Bacteriol. 180 (1998) 5932-5946
4. Osuna R., Lienau D., Hughes K.T., and Johnson R.C. Sequence, regulation, and functions of Fis in Salmonella typhimurium. J. Bacteriol. 177 (1995) 2021-2032
5. Schneider R., Travers A., and Muskhelishvili G. Fis modulates growth phase-dependent topological transitions of DNA in Escherichia coli. Mol. Microbiol. 26 (1997) 519-530
6. Schneider R., Travers A., Kutateladze T., and Muskhelishvili G. A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli. Mol. Microbiol. 34 (1999) 953-964
7. Finkel S.E., and Johnson R.C. The Fis protein: it's not just for DNA inversion anymore. Mol. Microbiol. 6 (1992) 3257-3265
8. Weinreich M.D., and Reznikoff W.S. Fis plays a role in Tn5 and IS50 transposition. J. Bacteriol. 174 (1992) 4530-4537
9. Johnson R.C., Bruist M.F., and Simon M.I. Host protein requirements for in vitro site-specific DNA inversion. Cell 46 (1986) 531-539
10. Kahmann R., Rudt F., Koch C., and Mertens G. G inversion in bacteriophage Mu DNA is stimulated by a site within the invertase gene and a host factor. Cell 41 (1985) 771-780
11. Betermier M., Lefrere V., Koch C., Alazard R., and Chandler M. The Escherichia coli protein, Fis: specific binding to the ends of phage Mu DNA and modulation of phage growth. Mol. Microbiol. 3 (1989) 459-468
12. Dorgai L., Oberto J., and Weisberg R.A. Xis and Fis proteins prevent site-specific DNA inversion in lysogens of phage HK022. J. Bacteriol. 175 (1993) 693-700
13. Bradley M.D., Beach M.B., Jason de Koning A.P., Pratt T.S., and Osuna R. Global effects of Fis on Escherichia coli gene expression during different stages of growth. Microbiology 153 (2007) 2922-2940
14. Kelly A., Goldberg M.D., Carroll R.K., Danino V., Hinton J.C., and Dorman C.J. A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium. Microbiology 150 (2004) 2037-2053
15. Xu J., and Johnson R.C. Identification of genes negatively regulated by Fis: Fis and RpoS comodulate growth-phase-dependent gene expression in Escherichia coli. J. Bacteriol. 177 (1995) 938-947
16. Gonzalez-Gil G., Bringmann P., and Kahmann R. FIS is a regulator of metabolism in Escherichia coli. Mol. Microbiol. 22 (1996) 21-29
17. Bosch L., Nilsson L., Vijgenboom E., and Verbeek H. FIS-dependent trans-activation of tRNA and rRNA operons of Escherichia coli. Biochim. Biophys. Acta 1050 (1990) 293-301
18. Ross W., Thompson J.F., Newlands J.T., and Gourse R.L. E. coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. EMBO J. 9 (1990) 3733-3742
19. Falconi M., Prosseda G., Giangrossi M., Beghetto E., and Colonna B. Involvement of FIS in the H-NS-mediated regulation of virF gene of Shigella and enteroinvasive Escherichia coli. Mol. Microbiol. 42 (2001) 439-452
20. Prosseda G., Falconi M., Giangrossi M., Gualerzi C.O., Micheli G., and Colonna B. The virF promoter in Shigella: more than just a curved DNA stretch. Mol. Microbiol. 51 (2004) 523-537
21. Goldberg M.D., Johnson M., Hinton J.C., and Williams P.H. Role of the nucleoid-associated protein Fis in the regulation of virulence properties of enteropathogenic Escherichia coli. Mol. Microbiol. 41 (2001) 549-559
22. Sheikh J., Hicks S., Dall'Agnol M., Phillips A.D., and Nataro J.P. Roles for Fis and YafK in biofilm formation by enteroaggregative Escherichia coli. Mol. Microbiol. 41 (2001) 983-997
23. Wilson R.L., Libby S.J., Freet A.M., Boddicker J.D., Fahlen T.F., and Jones B.D. Fis, a DNA nucleoid-associated protein, is involved in Salmonella typhimurium SPI-1 invasion gene expression. Mol. Microbiol. 39 (2001) 79-88
24. Hubner P., and Arber W. Mutational analysis of a prokaryotic recombinational enhancer element with two functions. EMBO J. 8 (1989) 577-585
25. Feng J.A., Yuan H.A., Finkel S.E., Johnson R.C., Kaczor-Grzeskowiak M., and Dickerson R.E. In: Sarma R.H.S.a.M.H. (Ed). The Interaction of Fis Protein with its DNA Binding Sequences. Structure and Function vol. 2 (1992), Adenine Press, Schenectady
26. Pan C.Q., Finkel S.E., Cramton S.E., Feng J.A., Sigman D.S., and Johnson R.C. Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts. J. Mol. Biol. 264 (1996) 675-695
27. Feldman L.S., Shao Y.P., Meinhold D., Miller C., Colon W., and Osuna R. Common and variable contributions of Fis residues to high-affinity binding at different DNA sequences. J. Bacteriol. 188 (2006) 2081-2095
28. Kostrewa D., Granzin J., Koch C., Choe H.W., Raghunathan S., Wolf W., et al. Three-dimensional structure of the E. coli DNA-binding protein FIS. Nature 349 (1991) 178-180
29. Kostrewa D., Granzin J., Stock D., Choe H.W., Labahn J., and Saenger W. Crystal structure of the factor for inversion stimulation FIS at 2.0 A resolution. J. Mol. Biol. 226 (1992) 209-226
30. Safo M.K., Yang W.Z., Corselli L., Cramton S.E., Yuan H.S., and Johnson R.C. The transactivation region of the Fis protein that controls site-specific DNA inversion contains extended mobile beta-hairpin arms. EMBO J. 16 (1997) 6860-6873
31. Yuan H.S., Finkel S.E., Feng J.A., Kaczor-Grzeskowiak M., Johnson R.C., and Dickerson R.E. The molecular structure of wild-type and a mutant fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding. Proc. Natl Acad. Sci. USA 88 (1991) 9558-9562
32. Osuna R., Finkel S.E., and Johnson R.C. Identification of two functional regions in Fis: the N-terminus is required to promote Hin-mediated DNA inversion but not lambda excision. EMBO J. 10 (1991) 1593-1603
33. Koch C., Ninnemann O., Fuss H., and Kahmann R. The N-terminal part of the E. coli DNA binding protein FIS is essential for stimulating site-specific DNA inversion but is not required for specific DNA binding. Nucleic Acids Res. 19 (1991) 5915-5922
34. Sandmann C., Cordes F., and Saenger W. Structure model of a complex between the factor for inversion stimulation (fis) and DNA: modeling protein-DNA complexes with dyad symmetry and known protein structures. Proteins: Struct. Funct. Genet. 25 (1996) 486-500
35. Tzou W.S., and Hwang M.J. Modeling helix-turn-helix protein-induced DNA bending with knowledge-based distance restraints. Biophys. J. 77 (1999) 1191-1205
36. Bruist M.F., Glasgow A.C., Johnson R.C., and Simon M.I. Fis binding to the recombinational enhancer of the Hin DNA inversion system. Genes Dev. 1 (1987) 762-772
37. Bokal A.J., Ross W., Gaal T., Johnson R.C., and Gourse R.L. Molecular anatomy of a transcription activation patch: fis-RNA polymerase interactions at the Escherichia coli rrnB P1 promoter. EMBO J. 16 (1997) 154-162
38. Hengen P.N., Bartram S.L., Stewart L.E., and Schneider T.D. Information analysis of Fis binding sites. Nucleic Acids Res. 25 (1997) 4994-5002
39. Bokal A.J.t., Ross W., and Gourse R.L. The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter. J. Mol. Biol. 245 (1995) 197-207
40. Gille H., Egan J.B., Roth A., and Messer W. The FIS protein binds and bends the origin of chromosomal DNA replication, oriC, of Escherichia coli. Nucleic Acids Res. 19 (1991) 4167-4172
41. Thompson J.F., and Landy A. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucleic Acids Res. 16 (1988) 9687-9705
42. Hales L.M., Gumport R.I., and 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. 24 (1996) 1780-1786
43. Lundin M., Nehlin J.O., and Ronne H. Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1. Mol. Cell. Biol. 14 (1994) 1979-1985
44. Bailly C., Waring M.J., and Travers A.A. Effects of base substitutions on the binding of a DNA-bending protein. J. Mol. Biol. 253 (1995) 1-7
45. Grainger D.C., Hurd D., Goldberg M.D., and Busby S.J. Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res. 34 (2006) 4642-4652
46. Ball C.A., Osuna R., Ferguson K.C., and Johnson R.C. Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J. Bacteriol. 174 (1992) 8043-8056
47. Ninnemann O., Koch C., and Kahmann R. The E. coli fis promoter is subject to stringent control and autoregulation. EMBO J. 11 (1992) 1075-1083
48. Mallik P., Paul B.J., Rutherford S.T., Gourse R.L., and Osuna R. DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli. J. Bacteriol. 188 (2006) 5775-5782
49. Gosink K.K., Ross W., Leirmo S., Osuna R., Finkel S.E., Johnson R.C., and Gourse R.L. DNA binding and bending are necessary but not sufficient for fis-dependent activation of rrnB P1. J. Bacteriol. 175 (1993) 1580-1589
50. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual. 2nd edit. (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor
51. Prentki P., Pham M.H., and Galas D.J. Plasmid permutation vectors to monitor DNA bending. Nucleic Acids Res. 15 (1987) 10060
52. Brunelle A., and Schleif R.F. Missing contact probing of DNA-protein interactions. Proc. Natl Acad. Sci. USA 84 (1987) 6673-6676
53. Maxam A.M., and Gilbert W. A new method for sequencing DNA. Proc. Natl Acad. Sci. USA 74 (1977) 560-564