The Role of High Affinity Non-specific DNA Binding by Lrp in Transcriptional Regulation and DNA Organization

Journal of Molecular Biology

Volumn 369, Issue 5, 2007, Pages 1307-1317

  Peterson, Stacey N ^a   Dahlquist, Frederick W ^a   Reich, Norbert O ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

cooperative; Lrp; non specific binding; nucleoid associated proteins; transcriptional regulation

Indexed keywords

CELL PROTEIN; DNA; LEUCINE RESPONSIVE REGULATORY PROTEIN;

ARTICLE; BINDING AFFINITY; BINDING KINETICS; BINDING SITE; CARBOXY TERMINAL SEQUENCE; DNA BINDING; DNA DETERMINATION; DNA SEQUENCE; ENZYME SPECIFICITY; GEL MOBILITY SHIFT ASSAY; GENE FUNCTION; HYPOTHESIS; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION;

BACTERIA (MICROORGANISMS);

EID: 34248634008     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.04.023     Document Type: Article

References (40)

1. Calvo J.M., and Matthews R.G. The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli. Microbiol. Rev. 58 (1994) 466-490
2. Newman E.B., and Lin R. Leucine-responsive regulatory protein: a global regulator of gene expression in E. coli. Annu. Rev. Microbiol. 49 (1995) 747-775
3. Cui Y., Wang Q., Stormo G.D., and Calvo J.M. A consensus sequence for binding of Lrp to DNA. J. Bacteriol. 177 (1995) 4872-4880
4. Rhee K.Y., Parekh B.S., and Hatfield G.W. Leucine-responsive regulatory protein-DNA interactions in the leader region of the ilvGMEDA operon of Escherichia coli. J. Biol. Chem. 271 (1996) 26499-26507
5. Nou X., Braaten B., Kaltenbach L., and Low D.A. Differential binding of Lrp to two sets of pap DNA binding sites mediated by Pap I regulates Pap phase variation in Escherichia coli. EMBO J. 14 (1995) 5785-5797
6. Tapias A., Lopez G., and Ayora S. Bacillus subtilis LrpC is a sequence-independent DNA-binding and DNA-bending protein which bridges DNA. Nucl. Acids Res. 28 (2000) 552-559
7. Chen S., Rosner M.H., and Calvo J.M. Leucine-regulated self-association of leucine-responsive regulatory protein (Lrp) from Escherichia coli. J. Mol. Biol. 312 (2001) 625-635
8. Chen S., and Calvo J.M. Leucine-induced dissociation of Escherichia coli Lrp hexadecamers to octamers. J. Mol. Biol. 318 (2002) 1031-1042
9. Chen S., Hao Z., Bieniek E., and Calvo J.M. Modulation of Lrp action in Escherichia coli by leucine: effects on non-specific binding of Lrp to DNA. J. Mol. Biol. 314 (2001) 1067-1075
10. Cui Y., Midkiff M.A., Wang Q., and Calvo J.M. The leucine-responsive regulatory protein (Lrp) from Escherichia coli. Stoichiometry and minimal requirements for binding to DNA. J. Biol. Chem. 271 (1996) 6611-6617
11. Landgraf J.R., Wu J., and Calvo J.M. Effects of nutrition and growth rate on Lrp levels in Escherichia coli. J. Bacteriol. 178 (1996) 6930-6936
12. Willins D.A., Ryan C.W., Platko J.V., and Calvo J.M. Characterization of Lrp, and Escherichia coli regulatory protein that mediates a global response to leucine. J. Biol. Chem. 266 (1991) 10768-10774
13. Luijsterburg M.S., Noom M.C., Wuite G.J., and Dame R.T. The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J. Struct. Biol. 156 (2006) 262-272
14. Wang Q., and Calvo J.M. Lrp, a major regulatory protein in Escherichia coli, bends DNA and can organize the assembly of a higher-order nucleoprotein structure. EMBO J. 12 (1993) 2495-2501
15. Thaw P., Sedelnikova S.E., Muranova T., Wiese S., Ayora S., Alonso J.C., et al. Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family. Nucl. Acids Res. 34 (2006) 1439-1449
16. von Hippel P.H., Revzin A., Gross C.A., and Wang A. C. Non-specific DNA binding of genome regulating proteins as a biological control mechanism: I. The lac operon: equilibrium aspects. Proc. Natl Acad. Sci. USA 71 (1974) 4808-4812
17. Hernday A.D., Braaten B.A., and Low D.A. The mechanism by which DNA adenine methylase and PapI activate the pap epigenetic switch. Mol. Cell 12 (2003) 947-957
18. Peterson S.N., and Reich N.O. GATC flanking sequences regulate Dam activity: evidence for how Dam specificity may influence pap expression. J. Mol. Biol. 335 (2006) 459-472
19. Jen-Jacobson L. Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state. Biopolymers 44 (1997) 153-180
20. Koo H.S., Wu H.M., and Crothers D.M. DNA bending at adenine. Thymine tracts. Nature 320 (1986) 501-506
21. von Hippel P.H., and McGhee J.D. DNA-protein interactions. Annu. Rev. Biochem. 41 (1972) 231-300
22. Wang Q., and Calvo J.M. Lrp, a global regulatory protein of Escherichia coli, binds co-operatively to multiple sites and activates transcription of ilvIH. J. Mol. Biol. 229 (1993) 306-318
23. Dahlquist F.W. The meaning of Scatchard and Hill plots. Methods Enzymol. 48 (1978) 270-299
24. Leonard P.M., Smits S.H., Sedelnikova S.E., Brinkman A.B., de Vos W.M., van der O.J., et al. Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus. EMBO J. 20 (2001) 990-997
25. de los Rios S., and Perona J.J. Structure of the Escherichia coli leucine-responsive regulatory protein Lrp reveals a novel octameric assembly. J. Mol. Biol. 366 (2007) 1589-1602
26. Kawamura T., Le L.U., Zhou H., and Dahlquist F.W. Solution structure of Escherichia coli PapI, a key regulator of the pap pili phase variation. J. Mol. Biol. 365 (2007) 1130-1142
27. Newman E.B., D'Ari R., and Lin R.T. The leucine-Lrp regulon in E. coli: a global response in search of a raison d'etre. Cell 68 (1992) 617-619
28. D'Ari R., Lin R.T., and Newman E.B. The leucine-responsive regulatory protein: more than a regulator?. Trends Biochem. Sci. 18 (1993) 260-263
29. 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
30. Tupper A.E., Owen-Hughes T.A., Ussery D.W., Santos D.S., Ferguson D.J., Sidebotham J.M., et al. The chromatin-associated protein H-NS alters DNA topology in vitro. EMBO J. 13 (1994) 258-268
31. Lucht J.M., Dersch P., Kempf B., and Bremer E. Interactions of the nucleoid-associated DNA-binding protein H-NS with the regulatory region of the osmotically controlled proU operon of Escherichia coli. J. Biol. Chem. 269 (1994) 6578
32. Atlung T., and Ingmer H. H-NS: a modulator of environmentally regulated gene expression. Mol. Microbiol. 24 (1997) 7-17
33. Ali A.T., Iwata A., Nishimura A., Ueda S., and Ishihama A. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol. 181 (1999) 6361-6370
34. Feldman-Cohen L.S., Shao Y., 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
35. White-Ziegler C.A., Angus Hill M.L., Braaten B.A., van der Woude M.W., and Low D.A. Thermoregulation of Escherichia coli pap transcription: H-NS is a temperature-dependent DNA methylation blocking factor. Mol. Microbiol. 28 (1998) 1121-1137
36. Starcic-Erjavec M., van Putten J.P., Gaastra W., Jordi B.J., Grabner M., and Zgur Bertok D. H-NS and Lrp serve as positive modulators of traJ expression from the Escherichia coli plasmid pRK100. Mol. Genet. Genomics 270 (2003) 94-102
37. Sandman K., and Reeve J.N. Archaeal chromatin proteins: different structures but common function?. Curr. Opin. Microbiol. 8 (2005) 656-661
38. Brinkman A.B., Ettema T.J., de Vos W.M., and van der O.J. The Lrp family of transcriptional regulators. Mol. Microbiol. 48 (2003) 287-294
39. Ernsting B.R., Denninger J.W., Blumenthal R.M., and Matthews R.G. Regulation of the gltBDF operon of Escherichia coli: how is a leucine-insensitive operon regulated by the leucine-responsive regulatory protein?. J. Bacteriol. 175 (1993) 7160-7169
40. Braaten B.A., Nou X., Kaltenbach L.S., and Low D.A. Methylation patterns in pap regulatory DNA control pyelonephritis-associated pili phase variation in E. coli. Cell 76 (1994) 577-588