Protein-induced fit: The CRP activator protein changes sequence-specific DNA recognition by the CytR repressor, a highly flexible LacI member

EMBO Journal

Volumn 16, Issue 8, 1997, Pages 2108-2118

  Pedersen, Henrik ^a,b   Valentin Hansen, Poul ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

cAMP CRP; CytR; In vitro selection; Protein DNA interactions; Protein protein interactions

Indexed keywords

CYCLIC AMP BINDING PROTEIN; TISSUE FACTOR PATHWAY INHIBITOR;

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA SEQUENCE; ESCHERICHIA COLI; GENE REPRESSION; NONHUMAN; OPERATOR GENE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN PROTEIN INTERACTION; REPRESSOR GENE; TRANSCRIPTION INITIATION;

BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; CARRIER PROTEINS; CYCLIC AMP RECEPTOR PROTEIN; DNA; DNA FOOTPRINTING; ESCHERICHIA COLI PROTEINS; PROTEIN CONFORMATION; REPETITIVE SEQUENCES, NUCLEIC ACID; REPRESSOR PROTEINS;

ESCHERICHIA COLI;

EID: 0030998034     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.8.2108     Document Type: Article

References (42)

1. Barbier, C.S. and Short, S.A. (1993) Characterization of cytR mutations that influence oligomerization of mutant repressor subunits. J. Bacteriol., 175, 4625-4630.
2. Blackwell, T.K. and Weintraub, H. (1990) Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. Science, 250, 1104-1110.
3. Blatter, E.E., Ross, W., Tang, H., Gourse, R.L. and Ebright, R.H. (1994) Domain organization of RNA polymerase α subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell, 78, 889-896.
4. Cadwell, R.C. and Joyce, G.F. (1992) Randomization of genes by PCR mutagenesis. PCR Methods Applications, 2, 28-32.
5. Choi, K.Y. and Zalkin, H. (1994) Role of the purine repressor hinge sequence in repressor function. J. Bacteriol., 176, 1767-1772.
6. 3, thyroid hormone and retinoic acid receptors. Mol. Cell. Biol., 12, 4153-4163.
7. Crothers, D.M. and Steitz, T.A. (1992) Transcriptional activation by Escherichia coli CAP protein. In McKnight, S.L. and Yamamoto, K.R. (eds), Transcriptional Regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 501-534.
8. de Crombrugghe, B., Busby, S. and Buc, H. (1984) Cyclic AMP receptor protein: role in transcription activation. Science, 224, 831-838.
9. Ebright, R.H., Ebright, Y.W. and Gunasekera, A. (1989) Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E.coli lac DNA site. Nucleic Acids Res., 17, 10295-10305.
10. Eustance, R.J., Bustos, S.A. and Schleif, R.F. (1994) Reaching out: locating and lengthening the interdomain linker in AraC protein. J. Mol. Biol., 242, 330-338.
11. Friedman, A.M., Fischmann, T.O. and Steitz, T.A. (1995) Crystal structure of lac repressor core tetramer and its implications for DNA looping. Science, 268, 1721-1727.
12. Galas, D.J. and Schmitz, A. (1978) DNase footprinting: a simple method for detection of protein-DNA binding specificity. Nucleic Acids Res., 5, 3157-3170.
13. Gartenberg, M.R. and Crothers, D.M. (1988) DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature, 333, 824-829.
14. 2 promoter of Escherichia coli K-12. J. Bacteriol., 173, 5419-5430.
15. Ghosaini, L.R., Brown, A.M. and Sturtevant, J.M. (1988) Scanning calorimetric study of the thermal unfolding of catabolite activator protein from E.coli in the absence and presence of cyclic mononucleotides. Biochemistry, 27, 5257-5261.
16. Herr, W. and Cleary, M.A. (1995) The POU domain: versatility in transcriptional regulation by a flexible two-in-one DNA-binding domain. Genes Dev., 9, 1679-1693.
17. Holst, B., Søgaard-Andersen, L., Pedersen, H. and Valentin-Hansen, P. (1992) The cAMP-CRP/CytR nucleoprotein complex in Escherichia coli: two pairs of closely linked binding sites for the cAMP-CRP activator complex are involved in combinatorial regulation of the cdd promoter. EMBO J., 11, 3635-3643.
18. Kristensen, H.-H., Valentin-Hansen, P. and Søgaard-Andersen, L. (1996) CytR/cAMP-CRP nucleoprotein formation in E.coli: the CytR repressor binds its operator as a stable dimer in a ternary complex with cAMP-CRP. J. Mol. Biol., 260, 113-119.
19. Kroeger, P.E. and Morimoto, R.I. (1994) Selection of new HSF1 and HSF2 DNA-binding sites reveals differences in trimer cooperativity. Mol. Cell. Biol. 14, 7592-7603.
20. Lewis, M., Chang, G., Horton, N.C., Kercher, M.A., Pace, H.C., Schumacher, M.A., Brennan, R.G. and Lu, P. (1996) Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science, 271, 1247-1254.
21. Liu-Johnson, H.-N., Gartenberg, M.R. and Crothers, D.M. (1986) The DNA-binding domain and bending angle of E.coli CAP protein. Cell, 47, 995-1005.
22. Mavrothalassitis, G., Beal, G. and Papas, T.S. (1990) Defining target sequences of DNA-binding proteins by random selection and PCR: determination of the GCN4 binding sequence repertoire. DNA Cell Biol., 9, 783-788.
23. Nagadoi, A. et al. (1995) Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain. Structure, 3, 1217-1224.
24. Nørregaard-Madsen, M, Mygind, B., Pedersen, R., Valentin-Hansen, P. and Søgaard-Andersen, L. (1994) The gene encoding the periplasmic cyclophilin homologue, PPIaseA, in Escherichia coli, is expressed from four promoters, three of which are activated by the cAMP-CRP complex and negatively regulated by the CytR repressor. Mol. Microbiol. 14, 989-997.
25. Pedersen, H., Søgaard-Andersen, L., Holst, B. and Valentin-Hansen, P. (1991) Heterologous cooperativity in Escherichia coli: the CytR repressor both contacts DNA and the cAMP receptor protein when binding to the deoP2 promoter. J. Biol. Chem., 266, 17804-17808.
26. Pedersen, H., Søgaard-Andersen, L., Holst, B., Gerlach, P., Bremer, E. and Valentin-Hansen, P. (1992) cAMP-CRP activator complex and the CytR repressor protein bind co-operatively to the cytRP promoter in Escherichia coli and CytR antagonizes the cAMP-CRP-induced DNA bend. J. Mol. Biol., 227, 396-406.
27. Pedersen, H., Dall, J., Dandanell, G. and Valentin-Hansen, P. (1995) Gene regulatory modules in Escherichia coli: nucleoprotein complexes formed by cAMP-CRP and CytR at the nupG promoter. Mol. Microbiol., 17, 843-853.
28. Pollock, R. and Treisman, R. (1990) A sensitive method for the determination of protein-DNA binding specificities. Nucleic Acids Res., 18, 6197-6204.
29. Rasmussen, P.B., Søgaard-Andersen, L. and Valentin-Hansen, P. (1993) Identification of the nucleotide sequence recognized by the cAMP-CRP dependent CytR repressor protein in the deoP2 promoter in E.coli. Nucleic Acids Res., 21, 879-885.
30. Schumacher, M.A., Choi, K.Y., Zalkin, H. and Brennan, R.G. (1994) Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by α helices. Science, 266, 763-770.
31. Smith, D.L. and Johnson, A.D. (1992) A molecular mechanism for combinatorial control in yeast: MCM1 protein sets the spacing and orientation of the homeodomains of an α2 dimer. Cell, 68, 133-142.
32. Søgaard-Andersen, L. and Valentin-Hansen, P. (1993) Protein-protein interactions in gene regulation: the cAMP-CRP complex sets the specificity of a second DNA-binding protein, the CytR repressor. Cell, 75, 557-566.
33. Søgaard-Andersen, L., Møllegaard, N.E., Douthwaite, S.R. and Valentin-Hansen, P. (1990) Tandem DNA-bound cAMP-CRP complexes are required for transcriptional repression of the deoP2 promoter by the CytR repressor in Escherichia coli. Mol. Microbiol., 4, 1595-1601.
34. Søgaard-Andersen, L., Mironov, A.S., Pedersen, H., Sukhodelets, V.V. and Valentin-Hansen, P. (1991a) Single amino acid substitutions in the cAMP receptor protein specifically abolish regulation by the CytR repressor in Escherichia coli. Proc. Natl Acad. Sci. USA, 88, 4921-4925.
35. Søgaard-Andersen, L., Pedersen, H., Holst, B. and Valentin-Hansen, P. (1991b) A novel function of the cAMP-CRP complex in Escherichia coli: cAMP-CRP functions as an adaptor for the CytR repressor in the deo operon. Mol. Microbiol., 5, 969-975.
36. Valentin-Hansen, P. (1982) Tandem CRP binding sites in the deo operon of Escherichia coli K-12. EMBO J., 1, 1049-1054.
37. Valentin-Hansen, P., Larsen, J.E.L., Højrup, P., Short, S.A., Barbier, C.S. (1986) Nucleotide sequence of the CytR regulatory gene of E.coli K-12. Nucleic Acids Res., 14, 2215-2228.
38. Valentin-Hansen, P., Søgaard-Andersen, L. and Pedersen, H. (1996) A flexible partnership: the CytR anti-activator and the cAMP-CRP activator protein, comrades in transcriptional control. Mol. Microbiol., 20, 461-466.
39. Verrijzer, C.P. Alkema, M.J., van Weperen, W.W., van Leeuwen, H.C., Strating, M.J.J. and van der Vliet, P.C. (1992) The DNA binding specificity of the bipartite POU domain and its subdomains. EMBO J., 11, 4993-5003.
40. Vidal-Ingigliardi, D., Richet, E. and Raibaud, O. (1991) Two MalT binding sites in direct repeat: a structural motif involved in the activation of all promoters of the maltose operon in Escherichia coli and Klebsiella pneumoniae. J. Mol. Biol., 218, 323-334.
41. Wade-Jardetzky, N., Bray, R.P., Conover, W.W., Jardetzky, O., Geisler, N. and Weber, K. (1979) Differential mobility of the N-termmal headpiece in the lac-repressor protein. J. Mol. Biol., 128, 259-264.
42. Weickert, M.J. and Adhya, S. (1992) A family of bacterial regulators homologous to Gal and Lac repressors. J. Biol. Chem., 267, 15869-15874.