Architecture of a Fur binding site: A comparative analysis

Journal of Bacteriology

Volumn 185, Issue 7, 2003, Pages 2194-2202

  Lavrrar, Jennifer L ^a   McIntosh, Mark A ^a  

^a University of Missouri   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; REGULATOR PROTEIN;

ARTICLE; BASE PAIRING; BINDING SITE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA SEQUENCE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; STOICHIOMETRY; TRANSCRIPTION REGULATION;

BACTERIAL PROTEINS; BASE PAIRING; BASE SEQUENCE; BINDING SITES; DIMERIZATION; DNA; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ESCHERICHIA COLI PROTEINS; MEMBRANE TRANSPORT PROTEINS; MODELS, MOLECULAR; PERIPLASMIC PROTEINS; REPRESSOR PROTEINS;

ESCHERICHIA COLI; NEGIBACTERIA; SYNTHETIC CONSTRUCT;

EID: 0037381732     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.7.2194-2202.2003     Document Type: Article

References (45)

1. Adrait, A., L. Jacquamet, L. L. Pape, A. Gonzalez de Peredo, D. Aberdam, J. L. Hazemann, J. M. Latour, and I. Michaud-Soret. 1999. Spectroscopic and saturation magnetization properties of the manganese- and cobalt-substituted Fur (ferric uptake regulation) protein from Escherichia coli. Biochemistry 38:6248-6260.
2. Alekshun, M. N., S. B. Levy, T. R. Mealy, B. A. Seaton, and J. F. Head. 2001. The crystal structure of MarR, a regulator of multiple antibiotic resistance, at 2.3 Å resolution. Nat. Struct. Biol. 8:710-714.
3. Althaus, E. W., C. E. Outten, K. E. Olson, H. Cao, and T. V. O'Halloran. 1999. The ferric uptake regulation (Fur) repressor is a zinc metalloprotein. Biochemistry 38:6559-6569.
4. Bagg, A., and J. Neilands. 1987. Molecular mechanism of regulation of siderophore-mediated iron assimilation. Microbiol. Rev. 51:509-518.
5. Baichoo, N., and J. D. Helmann. 2002. Recognition of DNA by Fur: a reinterpretation of the Fur box consensus sequence. J. Bacteriol. 184:5826-5832.
6. Boyd, J., M. N. Oza, and J. R. Murphy. 1990. Molecular cloning and DNA sequence analysis of a diphtheria tox iron-dependent regulatory element (dtxR) from Corynebacterium diphtheriae. Proc. Natl. Acad. Sci. USA 87:5968-5972.
7. Brickman, T. J., B. A. Ozenberger, and M. A. McIntosh. 1990. Regulation of divergent transcription from the iron-responsive fepB-entC promoter-operator regions in Escherichia coli. J. Mol. Biol. 212:669-682.
8. Calderwood, S. B., and J. J. Mekalanos. 1987. Iron regulation of Shiga-like toxin expression in Escherichia coli is mediated by the fur locus. J. Bacteriol. 169:4759-4764.
9. Christotfersen, C. A., T. J. Brickman, I. Hook-Barnard, and M. A. McIntosh. 2001. Regulatory architecture of the iron-regulated fepD-ybdA bidirectional promoter region in Escherichia coli. J. Bacteriol. 183:2059-2070.
10. Cicero, M. P., S. T. Hubl, C. J. Harrison, O. Littlefield, J. A. Hardy, and H. C. M. Nelson. 2001. The wing in yeast heat shock transcription factor (HSF) DNA-binding domain is required for full activity. Nucleic Acids Res. 29:1715-1723.
11. Coy, M., and J. B. Neilands. 1991. Structural dynamics and functional domains of the Fur protein. Biochemistry 30:8201-8210.
12. de Lorenzo, V., F. Giovannini, M. Herrero, and J. B. Neilands. 1988. Metal ion regulation of gene expression. Fur repressor-operator interaction at the promoter region of the aerobactin system of pCoIV-K30. J. Mol. Biol. 203:875-884.
13. de Lorenzo, V., M. Herrero, F. Giovannini, and J. B. Neilands. 1988. Fur (ferric uptake regulation) protein and CAP (catabolite-activator protein) modulate transcription of fur gene in Escherichia coli. Eur. J. Biochem. 173:537-546.
14. Escolar, L., J. Pérez-Martin, and V. de Lorenzo. 1998. Binding of the Fur (ferric uptake regulator) repressor of Escherichia coli to arrays of the GATAAT sequence. J. Mol. Biol. 283:537-547.
15. Escolar, L., J. Pérez-Martin, and V. de Lorenzo. 2000. Evidence of an unusually long operator for the Fur repressor in the aerobactin promoter of Escherichia coli. J. Biol. Chem. 275:24709-24714.
16. Ferguson, K. A. 1964. Starch-gel electrophoresis - application to the classification of pituitary proteins and polypeptides. Metabolism 13:985-1002.
17. Fréchon, D., and E. L. Cam. 1994. Fur (ferric uptake regulation) protein interaction with target DNA: comparison of gel retardation, footprinting and electron microscopy analyses. Biochem. Biophys. Res. Commun. 201:346-355.
18. Gajiwala, K. S., and S. K. Burley. 2000. Winged helix proteins. Opin. Struct. Biol. 10:110-116.
19. Gonzalez de Peredo, A., C. Saint-Pierre, J. M. Latour, I. Michaud-Soret, and E. Forest. 2001. Conformational changes of the ferric uptake regulation protein upon metal activation and DNA binding: first evidence of structural homologies with the diphtheria toxin repressor. J. Mol. Biol. 310:83-91.
20. Griggs, D. W., and J. Konisky. 1989. Mechanism for iron-regulated transcription of the Escherichia coli cir gene: metal-dependent binding of Fur protein to the promoter. J. Bacteriol. 171:1048-1054.
21. Hendrickson, W., and R. Schleif. 1985, A dimer of AraC protein contacts three adjacent major groove regions of the aral DNA site. Proc. Natl. Acad. Sci. USA 82:3129-3133.
22. Holm, L., C. Sander, H. Ruerjans, M. Schnarr, R. Fogh, R. Boelens, and R. Kaptein. 1994. LexA repressor and iron uptake regulator from Escherichia coli: new members of the CAP-like DNA binding domain superfamily. Protein Eng. 7:1449-1453.
23. Hunt, M. D., G. S. Pettis, and M. A. McIntosh. 1994. Promoter and operator determinants for Fur-mediated iron regulation in the bidirectional fepA-fes control region of the Escherichia coli enterobactin gene system. J. Bacteriol. 176:3944-3955.
24. Jacquamet, L., D. Aberdam, A. Adrait, J. L. Hazemann, and J. M. M.-S. I. Latour. 1998. X-ray absorption spectroscopy of a new zinc site in the Fur protein from Escherichia coli. Biochemistry 37:2564-2571.
25. Lavrrar, J. L., C. A. Christotfersen, and M. A. McIntosh. 2002. Fur-DNA interactions at the bidirectional fepDGC-entS promoter region in Escherichia coli. J. Mol. Biol. 322:983-995.
26. Lee, J. H., T. Wang, K. Ault, J. Liu, M. P. Schmitt, and R. K. Holmes. 1997. Identification and characterization of three new promoter/operators from Corynebacterium diphtheriae that are regulated by the diphtheria toxin repressor (DtxR) and iron. Infect. Immun. 65:4273-4280.
27. Litwin, C. M., and S. B. Calderwood. 1993. Role of iron in regulation of virulence genes. Clin. Microbiol. Rev. 6:137-149.
28. Martinez-Hackert, E., and A. M. Stock. 1997. Structural relationships in the OmpR family of winged-helix transcription factors. J. Mol. Biol. 269:301-312.
29. Michaud-Soret, I., A. Adrait, M. Jaquinod, E. Forest, D. Touati, and J. M. Latour. 1997. Electrospray ionization mass spectrometry analysis of the apo- and metal-substituted forms of the Fur protein. FEBS Lett. 413:473-476.
30. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
31. Niederhoffer, E. C., C. M. Naranjo, K. L. Bradley, and J. A. Fee. 1990. Control of Escherichia coli superoxide dismutase (sodA and sodB) genes by the ferric uptake regulation (fur) locus. J. Bacteriol. 172:1930-1938.
32. Ochsner, U. A., and M. L. Vasil. 1996. Gene repression by the ferric uptake regulator in Pseudomonas aeruginosa: Cycle selection of iron-regulated genes. Proc. Natl. Acad. Sci. USA 93:4409-4414.
33. Orchard, K., and G. E. May. 1993. An EMSA-based method for determining the molecular weight of a protein- DNA complex. Nucleic Acids Res. 21:3335-3336.
34. Pohl, E., R. K. Holmes, and W. G. J. Hol. 1999. Crystal structure of a cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal-binding SH3-like domain. J. Mol. Biol. 292:653-667.
35. Ptashne, M. 1986. A genetic switch. Blackwell Scientific, London, England.
36. Saito, T., and R. J. P. Williams. 1991. The binding of the ferric uptake regulation protein to a DNA fragment. Eur. J. Biochem. 197:43-47.
37. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
38. Schmitt, M. P., and R. K. Holmes. 1991. Characterization of a defective diphtheria toxin repressor (dtxR) allele and analysis of dtxR transcription in wild-type and mutant strains of Corynebacterium diphtheriae. Infect. Immun. 39:3903-3908.
39. Schmitt, M. P., and R. K. Holmes. 1994. Cloning, sequence, and footprint analysis of two promoter/operators from Corynebacterium diphtheriae that are regulated by the diphtheria toxin repressor (DtxR) and iron. J. Bacteriol. 176:1141-1149.
40. Stojiljkovic, I., A. J. Bäumler, and K. Hantke. 1994. Fur regulon in Gram-negative bacteria: identification and characterization of new iron-regulated Eschenchia coli genes by a Fur titration assay. J. Mol. Biol. 236:531-545.
41. Tao, X., and J. R. Murphy. 2002. Binding of the metalloregulatory protein DtxR to the diphtheria tox operator requires a divalent heavy metal ion and protects the palindromic sequence from DNase I digestion. J. Biol. Chem. 267:21761-21764.
42. Tardat, B., and D. Touati. 1991. Two global regulators repress the anaerobic expression of MnSOD in Escherichia coli: Fur (ferric uptake regulation) and Arc (aerobic respiration control). Mol. Microbiol. 5:455-465.
43. Tardat, B., and D. Touati. 1993. Iron and oxygen regulation of Escherichia coli MnSOD expression: competition between the global regulators Fur and ArcA for binding to DNA. Mol. Microbiol. 9:53-63.
44. Vassinova, N., and D. Kozyrev. 2000. A method for direct cloning of Fur-regulated genes: identification of seven new Fur-regulated loci in Escherichia coli. Microbiology 146:3171-3182.
45. White, A., X. Ding, J. C. vander Spek, J. R. Murphy, and D. Ringe. 1998. Structure of the metal-ion-activated diphtheria toxin repressor/Tox operator complex. Nature 394:502-506.