Searching for the nik Operon: How a ligand-responsive transcription factor hunts for its DNA binding site

Biochemistry

Volumn 49, Issue 36, 2010, Pages 7757-7763

  Phillips, Christine M ^a,b   Stultz, Collin M ^a,b,c   Drennan, Catherine L ^a,d  

^a Department of Chemistry ^*  (United States)

^b Research Laboratory of Electronics   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC LEVELS; CELLULAR HOMEOSTASIS; CELLULAR MODEL; COMPUTATIONAL STUDIES; CURRENT MODELS; DIFFUSION LIMITS; DNA BINDING; DNA BINDING SEQUENCE; DNA BINDING SITE; E. COLI; MEDIATED TRANSCRIPTION;

BINDING ENERGY; BINDING SITES; BIOCHEMISTRY; DNA; ESCHERICHIA COLI; GENES; LIGANDS; TRANSCRIPTION FACTORS;

TRANSCRIPTION;

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NIKR; UNCLASSIFIED DRUG; DNA; ESCHERICHIA COLI PROTEIN; LIGAND; NIKR PROTEIN, E COLI; REPRESSOR PROTEIN;

BINDING SITE; ESCHERICHIA COLI; OPERON; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN STRUCTURE; REVIEW; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; LIGANDS; MODELS, MOLECULAR; OPERON; PROTEIN CONFORMATION; REPRESSOR PROTEINS;

ESCHERICHIA COLI;

EID: 77956416750     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi100947k     Document Type: Review

References (40)

1. Schreiter, E. R., Sintchak, M. D., Guo, Y., Chivers, P. T., Sauer, R. T., and Drennan, C. L. (2003) Crystal structure of nickel-responsive transcription factor NikR Nat. Struct. Biol. 10, 794-799
2. Chivers, P. T. and Sauer, R. T. (2002) NikR Repressor: High-Affinity Nickel Binding to the C-Terminal Domain Regulates Binding to Operator DNA Chem. Biol. 9, 1141-1148
3. Wang, S. C., Dias, A. V., Bloom, S. L., and Zamble, D. B. (2004) Selectivity of Metal Binding and Metal-Induced Stability of Escherichia coli NikR Biochemistry 43, 10018-10028
4. Bloom, S. L. and Zamble, D. B. (2004) Metal-Selective DNA-Binding Response of Escherichia coli NikR Biochemistry 43, 10029-10038
5. Navarro, C., Wu, L. F., and Mandrand-Berthelot, M.-A. (1993) The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system for nickel Mol. Microbiol. 9, 1181-1191
6. 2+-dependent interaction of NikR with wild-type and mutant operator sites J. Biol. Chem. 275, 19735-19741
7. Phillips, C. M., Schreiter, E. R., Stultz, C. M., and Drennan, C. L. (2010) Structural Basis of Low Affinity Nickel Binding to the Nickel-Responsive Transcription Factor NikR from Escherichia coli Biochemistry 49, in press. (doi: 10.1021/bi100923j).
8. Wang, S. C., Li, Y., Robinson, C. V., and Zamble, D. B. (2010) Potassium is Critical for the Ni(II)-Responsive DNA-Binding Activity of Escherichia coli NikR J. Am. Chem. Soc. 132, 1506-1507
9. Phillips, C. M., Nerenberg, P. S., Drennan, C. L., and Stultz, C. M. (2009) Physical Basis of Metal-Binding Specificity in Escherichia coli NikR J. Am. Chem. Soc. 131, 10220-10228
10. Schreiter, E. R., Wang, S. C., Zamble, D. B., and Drennan, C. L. (2006) NikR-operator complex structure and the mechanism of repressor activation by metal ions Proc. Natl. Acad. Sci. U.S.A. 103, 13676-13681
11. Chivers, P. T. and Sauer, R. T. (1999) NikR is a ribbon-helix-helix DNA-binding protein Protein Sci. 8, 2494-2500
12. Phillips, C. M., Schreiter, E. R., Guo, Y., Wang, S. C., Zamble, D. B., and Drennan, C. L. (2008) Structural Basis of the Metal Specificity for Nickel Regulatory Protein NikR Biochemistry 47, 1938-1946
13. Abraham, L. O., Li, Y., and Zamble, D. B. (2006) The metal- and DNA-binding activities of Helicobacter pylori NikR J. Inorg. Biochem. 100, 1005-1014
14. Dian, C., Schauer, K., Kapp, U., McSweeney, S. M., Labigne, A., and Terradot, L. (2006) Structural Basis of the Nickel Response in Helicobacter pylori: Crystal Structures of HpNikR in Apo and Nickel-bound States J. Mol. Biol. 361, 715-730
15. Dosanjh, N. S., Hammerbacher, N. A., and Michel, S. L. (2007) Characterization of the Helicobacter pylori NikR-P(ureA) DNA interaction: Metal ion requirements and sequence specificity Biochemistry 46, 2520-2529
16. Dosanjh, N. S., West, A. L., and Michel, S. L. (2009) Helicobacter pylori NikRs interaction with DNA: A two-tiered mode of recognition Biochemistry 48, 527-536
17. Ernst, F. D., Kuipers, E. J., Heijens, A., Sarwari, R., Stoof, J., Penn, C. W., Kusters, J. G., and van Vliet, A. H. M. (2005) The Nickel-Responsive Regulator NikR controls Activation and Repression of Gene Transcription in Helicobacter pylori Infect. Immun. 73, 7252-7258
18. Ernst, F. D., Stoof, J., Horrevoets, W. M., Kuipers, E. J., Kusters, J. G., and van Vliet, A. H. M. (2006) NikR Mediates Nickel-Responsive Transcriptional Repression of the Helicobacter pylori Outer Membrane Proteins FecA3 (HP1400) and FrpB4 (HP1512) Infect. Immun. 74, 6821-6828
19. 2+ binding properties of Helicobacter pylori NikR Chem. Commun., 3649-3651
20. Phillips, C. M. and Drennan, C. L. (2008) Nickel Regulatory Transcription Factor, NikR. In Handbook of Metalloproteins (Messerschmidt, A., Ed.) John Wiley & Sons, Ltd., New York.
21. Wang, S. C., Dias, A. V., and Zamble, D. B. (2009) The "metallo-specific" response of proteins: A perspective based on the Escherichia coli transcriptional regulator NikR Dalton Trans., 2459-2466
22. de Pina, K., Desjardin, V., Mandrand-Berthelot, M.-A., Giordano, G., and Wu, L. F. (1999) Isolation and Characterization of the nikR Gene Encoding a Nickel-Responsive Regulator in Escherichia coli J. Bacteriol. 181, 670-674
23. Leitch, S., Bradley, M. J., Rowe, J. L., Chivers, P. T., and Maroney, M. J. (2007) Nickel-Specific Response in the Transcriptional Regulator, Escherichia coli NikR J. Am. Chem. Soc. 129, 5085-5095
24. Riggs, A. D., Bourgeoi, S., and Cohn, M. (1970) The Lac Repressor-Operator Interaction. 3. Kinetic Studies J. Mol. Bio. 53, 401-417
25. Berg, O. G., Winter, R. B., and Vonhippel, P. H. (1981) Diffusion-Driven Mechanisms of Protein Translocation on Nucleic-Acids. 1. Models and Theory Biochemistry 20, 6929-6948
26. Richter, P. H. and Eigen, M. (1974) Diffusion Controlled Reaction-Rates in Spheroidal Geometry: Application to Repressor-Operator Association and Membrane-Bound Enzymes Biophys. Chem. 2, 255-263
27. Berg, O. G. and Blomberg, C. (1976) Association Kinetics with Coupled Diffusional Flows: Special Application to Lac Repressor-Operator System Biophys. Chem. 4, 367-381
28. Blainey, P. C., van Oijent, A. M., Banerjee, A., Verdine, G. L., and Xie, X. S. (2006) A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA Proc. Natl. Acad. Sci. U.S.A. 103, 5752-5757
29. Elf, J., Li, G. W., and Xie, X. S. (2007) Probing transcription factor dynamics at the single-molecule level in a living cell Science 316, 1191-1194
30. Gorman, J., Chowdhury, A., Surtees, J. A., Shimada, J., Reichman, D. R., Alani, E., and Greene, E. C. (2007) Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6 Mol. Cell 28, 359-370
31. Gorman, J. and Greene, E. C. (2008) Visualizing one-dimensional diffusion of proteins along DNA Nat. Struct. Mol. Biol. 15, 768-774
32. Gowers, D. M., Wilson, G. G., and Halford, S. E. (2005) Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA Proc. Natl. Acad. Sci. U.S.A. 102, 15883-15888
33. Kim, J. G., Takeda, Y., Matthews, B. W., and Anderson, W. F. (1987) Kinetic Studies on Cro Repressor Operator DNA Interaction J. Mol. Biol. 196, 149-158
34. McKinney, K., Mattia, M., Gottifredi, V., and Prives, C. (2004) p53 linear diffusion along DNA requires its C terminus Mol. Cell 16, 413-424
35. Winter, R. B., Berg, O. G., and Vonhippel, P. H. (1981) Diffusion-Driven Mechanisms of Protein Translocation on Nucleic Acids. 3. The Escherichia coli Lac Repressor-Operator Interaction: Kinetic Measurements and Conclusions Biochemistry 20, 6961-6977
36. Graneli, A., Yeykal, C. C., Robertson, R. B., and Greene, E. C. (2006) Long-distance lateral diffusion of human Rad51 on double-stranded DNA Proc. Natl. Acad. Sci. U.S.A. 103, 1221-1226
37. Wang, Y. M., Austin, R. H., and Cox, E. C. (2006) Single molecule measurements of repressor protein 1D diffusion on DNA Phys. Rev. Lett. 97, 048302
38. Tafvizi, A., Huang, F., Leith, J. S., Fersht, A. R., Mirny, L. A., and van Oijen, A. M. (2008) Tumor suppressor p53 slides on DNA with low friction and high stability Biophys. J. 95, L1-L3
39. Slutsky, M. and Mirny, L. A. (2004) Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential Biophys. J. 87, 4021-4035
40. Epstein, W. and Schultz, S. G. (1966) Cation transport in Escherichia coli. VI. K exchange J. Gen. Physiol. 49, 469-481