CAMP receptor protein from escherichia coli as a model of signal transduction in proteins - A review

Journal of Molecular Microbiology and Biotechnology

Volumn 17, Issue 1, 2009, Pages 1-11

  Fic, E ^a   Bonarek, P ^a   Gorecki, A ^a   Kedracka Krok, S ^a   Mikolajczak, J ^a   Polit, A ^a   Tworzydlo, M ^a   Dziedzicka Wasylewska, M ^a   Wasylewski, Z ^a  

^a JAGIELLONIAN UNIVERSITY   (Poland)

Author keywords

Allosteric activation; Cyclic AMP binding; DNA binding; Signal transduction; Transcription activation

Indexed keywords

CYCLIC AMP; CYCLIC AMP BINDING PROTEIN; DNA; CRP PROTEIN, E COLI; ESCHERICHIA COLI PROTEIN;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; BINDING AFFINITY; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; CRYSTALLIZATION; DNA SEQUENCE; ESCHERICHIA COLI; NONHUMAN; PROMOTER REGION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; SIGNAL TRANSDUCTION; SITE DIRECTED MUTAGENESIS; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; X RAY CRYSTALLOGRAPHY; ALLOSTERISM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PHYSIOLOGY;

ESCHERICHIA COLI;

ALLOSTERIC REGULATION; CYCLIC AMP; CYCLIC AMP RECEPTOR PROTEIN; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; SIGNAL TRANSDUCTION;

EID: 67649400754     PISSN: 14641801     EISSN: None     Source Type: Journal    
DOI: 10.1159/000178014     Document Type: Review

References (74)

1. Aiba H, Fujimoto S, Ozaki N: Molecular cgloning and nucleotide sequencing of the gene for Escherichia coli cAMP receptor protein. Nucleic Acids Res 1982;10:1345-1362.
2. Anderson WB, Schneider AB, Emmer M, Perlman RL, Pastan I: Purification of and properties of the cyclic adenosine 3′,5′-monophosphate receptor protein which mediates cyclic adenosine 3′,5′-monophosphate- dependent gene transcription in Escherichia coli. J Biol Chem 1971;246:5929-5937.
3. Baichoo N, Heyduk T: DNA-induced conformational changes in cyclic AMP receptor protein: detection and mapping by a protein footprinting technique using multiple chemical proteases. J Mol Biol 1999;290:37-48.
4. Baker CH, Tomlinson SR, Garcia AE, Harman JG: Amino acid substitution at position 99 affects the rate of CRP subunit exchange. Biochemistry 2001;40:12329-12338.
5. Berrera M, Pantano S, Carloni P: Catabolite activator protein in aqueous solution: a molecular simulation study. J Phys Chem B 2007;111:1496-1501.
6. Blaszczyk U, Polit A, Guz A, Wasylewski Z: Interaction of cAMP receptor protein from Escherichia coli with cAMP and DNA studied by dynamic light scattering and time-resolved fluorescence anisotropy methods. J Protein Chem 2001;20:601-610.
7. Blaszczyk U, Wasylewski Z: Interaction of cAMP receptor protein from Escherichia coli with cAMP and DNA studied by differential scanning calorimetry. J Protein Chem 2003;22:285-293.
8. Brennan RG, Matthews BW: The helix-turn-helix DNA-binding motif. J Biol Chem 1989;264:1903-1906.
9. Brown AM, Crothers DM: Modulation of the stability of a gene-regulatory protein dimer by DNA and cAMP. Proc Natl Acad Sci USA 1989;86:7387-7391.
10. Busby S, Ebright RH: Transcription activation at class II CAP-dependent promoters. Mol Microbiol 1997;23:853-859.
11. Busby S, Ebright RH: Transcription activation by catabolite activator protein. J Mol Biol 1999;293:199-213.
12. Chen R, Ching Lee J: Functional roles of loops 3 and 4 in the cyclic nucleotide-binding domain of cyclic AMP receptor protein from Escherichia coli. J Biol Chem 2003;278:13235-13243.
13. Cheng X, Ching Lee J: Interactive and dominant effects of residues 128 and 141 on cyclic nucleotide and DNA bindings in Escherichia coli cAMP receptor protein. J Biol Chem 1998;273:705-712.
14. Dai J, Lin SH, Kemmis C, Chin AJ, Lee JC: Interplay between site-specific mutations and cyclic nucleotides in modulating DNA recognition by Escherichia coli cyclic AMP receptor protein. Biochemistry 2004;43:8901-8910.
15. Dethiollaz S, Eichenberger P, Geiselmann J: Influence of DNA geometry on transcriptional activation in Escherichia coli. EMBO J 1996;15:5449-5458.
16. Dong A, Malecki JM, Lee L, Carpenter JF, Ching Lee J: Ligand-induced conformational and structural dynamics changes in Escherichia coli cyclic AMP receptor protein. Biochemistry 2002;41:6660-6667.
17. Ebright RH: Transcription activation at class I CAP-dependent promoters. Mol Microbiol 1993;8:797-802.
18. Ebright YW, Chen Y, Pendergrast PS, Ebright RH: Incorporation of an EDTA-metal complex at a rationally selected site within a protein: application to EDTA-iron DNA affinity cleaving with catabolite gene activator protein (CAP) and Cro. Biochemistry 1992;31:10664-10670.
19. Epstein W, Rothman-Denes LB, Hesse J: Adenosine 3′,5′-cyclic monophosphate as mediator of catabolite repression in Escherichia coli. Proc Natl Acad Sci USA 1975;72:2300-2304.
20. Fic E, Gorecki A, Wasylewski Z: Fluorescence quenching studies of conformational changes induced by cAMP and DNA binding to heterodimer of cyclic AMP receptor protein from Escherichia coli. Protein J 2007;26:457-466.
21. Fic E, Polit A, Wasylewski Z: Kinetic and structural studies of the allosteric conformational changes induced by binding of cAMP to the cAMP receptor protein from Escherichia coli. Biochemistry 2006;45:373-380.
22. 2 in non-crystalline environments show a subunit transition from the open to the closed conformation. Protein Sci 1996;5:62-71.
23. Gekko K, Obu N, Li J, Lee JC: A linear correlation between the energetics of allosteric communication and protein flexibility in the Escherichia coli cyclic AMP receptor protein revealed by mutation-induced changes in compressibility and amide hydrogen-deuterium exchange. Biochemistry 2004;43:3844-3852.
24. Giraud-Panis MJ, Toulme F, Blazy B, Maurizot JC, Culard F: Fluorescence study on the nonspecific binding of cyclic-AMP receptor protein to DNA: effect of pH. Biochimie 1994;76:133-139.
25. Gorshkova I, Moore JL, McKenney KH, Schwarz FP: Thermodynamics of cyclic nucleotide binding to the cAMP receptor protein and its T127L mutant. J Biol Chem 1995;270:21679-21683.
26. Gutierrez-Ríos RM, Freyre-Gonzalez JA, Resendis O, Collado-Vides J, Saier M, Gosset G: Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli. BMC Microbiol 2007;DOI: 10.1186/147-2180-7-53.
27. Harman JG: Allosteric regulation of the cAMP receptor protein. Biochim Biophys Acta 2001;1547:1-17.
28. Heyduk T, Lee JC, Ebright YW, Blatter EE, Zhou Y, Ebright RH: CAP interacts with RNA polymerase in solution in the absence of promoter DNA. Nature 1993;364:548-549.
29. Jacob F, Monod J: Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 1961;3:318-356.
30. Katouzian-Safadi M, Blazy B, Cremet JY, Le Caer JP, Rossier J, Charlier M: Photo-cross-linking of CRP to nonspecific DNA in the absence of cAMP. DNA interacts with both the N- and C-terminal parts of the protein. Biochemistry 1993;32:1770-1773.
31. Kim J, Adhya S, Garges S: Allosteric changes in the cAMP receptor protein of Escherichia coli: hinge reorientation. Proc Natl Acad Sci USA 1992;89:9700-9704.
32. Kolb A, Busby S, Buc H, Garges S, Adhya S: Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 1993;62:749-795.
33. Krueger S, Gregurick S, Shi Y, Wang S, Wladkowski BD, Schwarz FP: Entropic nature of the interaction between promoter bound CRP mutants and RNA polymerase. Biochemistry 2003;42:1958-1968.
34. Lin SH, Lee JC: Communications between the high-affinity cyclic nucleotide-binding sites in Escherichia coli cyclic AMP receptor protein: effect of single site mutations. Biochemistry 2002;41:11857-11867.
35. Lin SH, Lee JC: Determinants of DNA bending in the DNA-cyclic AMP receptor protein complexes in Escherichia coli. Biochemistry 2003;42:4809-4818.
36. Malecki J, Wasylewski Z: Stability and kinetics of unfolding and refolding of cAMP receptor protein from Escherichia coli. Eur J Biochem 1997;243:660-669.
37. Malecki J, Wasylewski Z: The effect of Ser 128 substitution on the structure and stability of cAMP receptor protein from Escherichia coli. J Protein Chem 1998;17:219-228.
38. Malecki J, Polit A, Wasylewski Z: Kinetic studies of cAMP-induced allosteric changes in cyclic AMP receptor protein from Escherichia coli. J Biol Chem 2000;275:8480-8486.
39. McKay DB, Weber IT, Steitz TA: Structure of catabolite gene activator protein at 2.9-Å resolution. J Biol Chem 1982;257:9518-9524.
40. Merkel TJ, Dahl JL, Ebright RH, Kadner RJ: Transcription activation at the Escherichia coli uhpT promoter by the catabolite gene activator protein. J Bacteriol 1995;177:1712-1718.
41. Mukhopadhyay J, Sur R, Parrack P: Functional roles of the two cyclic AMP-dependent forms of cyclic AMP receptor protein from Escherichia coli. FEBS Lett 1999;453:215-218.
42. Niu W, Kim Y, Tau G, Heyduk T, Ebright RH: Transcription activation at class II CAP-dependent promoters: two interactions between CAP and RNA polymerase. Cell 1996;87:1123-1134.
43. Niu W, Zhou Y, Dong Q, Ebright YW, Ebright RH: Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). I. Saturation and alanine-scanning mutagenesis. J Mol Biol 1994;243:595-602.
44. Parkinson G, Wilson C, Gunasekera A, Ebright YW, Ebright RE, Berman HM: Structure of the CAP-DNA complex at 2.5-Å resolution: a complete picture of the protein-DNA interface. J Mol Biol 1996;260:395-408.
45. Passner JM, Schultz SC, Steitz TA: Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1-Å resolution. J Mol Biol 2000;304:847-859.
46. Passner JM, Steitz TA: The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer. Proc Natl Acad Sci USA 1997;94:2843-2847.
47. Polit A, Blaszczyk U, Wasylewski Z: Steady-state and time-resolved fluorescence studies of conformational changes induced by cyclic AMP and DNA binding to cyclic AMP receptor protein from Escherichia coli. Eur J Biochem 2003a;270:1413-1423.
48. Polit A, Bonarek P, Kepys B, Kedracka-Krok S, Gorecki A, Wasylewski Z: Kinetic studies of cAMP-induced allosteric changes in mutants T127I, S128A, and T127I/S128A of the cAMP receptor protein from Escherichia coli. J Biol Chem 2003b;278:43020-43026.
49. Pyles EA, Chin AJ, Lee JC: Escherichia coli cAMP receptor protein-DNA complexes. 1. Energetic contributions of half-sites and flanking sequences in DNA recognition. Biochemistry 1998;37:5194-5200.
50. Pyles EA, Lee JC: Escherichia coli cAMP receptor protein-DNA complexes. 2. Structural asymmetry of DNA bending. Biochemistry 1998;37:5201-5210.
51. Rhodius VA, West DM, Webster CL, Busby SJ, Savery NJ: Transcription activation at class II CRP-dependent promoters: the role of different activating regions. Nucleic Acids Res 1997;25:326-332.
52. Ryu S, Kim J, Adhya S, Garges S: Pivotal role of amino acid at position 138 in the allosteric hinge reorientation of cAMP receptor protein. Proc Natl Acad Sci USA 1993;90:75-79.
53. Salemme FR: A model for catabolite activator protein binding to supercoiled DNA. Proc Natl Acad Sci USA 1982;79:5263-5267.
54. Schultz SC, Shields GC, Steitz TA: Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 1991;253:1001-1007.
55. Scott SP, Harrison RW, Weber IT, Tanaka JC: Predicted ligand interactions of 3′5′-cyclic nucleotide-gated channel-binding sites: comparison of retina and olfactory binding site models. Protein Eng 1996;9:333-344.
56. Semsey S, Krishna S, Sneppen K, Adhya S: Signal integration in the galactose network of Escherichia coli. Mol Microbiol 2007;65:465-476.
57. Shabb JB, Corbin JD: Cyclic nucleotide-binding domains in proteins having diverse functions. J Biol Chem 1992;267:5723-5726.
58. Shen X, Tao W, Kong J, Yu S: The role of loops 3 and 4 in the interdomains and intersubunits communication of Escherichia coli cAMP receptor protein. Int J Biol Macromol 2008;42:372-379.
59. Søgaard-Andersen L, Mironov AS, Pedersen H, Sukhodelets VV, Valentin-Hansen P: Single amino acid substitutions in the cAMP receptor protein specifically abolish regulation by the CytR repressor in Escherichia coli. Proc Natl Acad Sci USA 1991;88:4921-4925.
60. Søgaard-Andersen L, Valentin-Hansen P: Protein-protein interactions in gene regulation: the cAMP-CRP complex sets the specificity of a second DNA-binding protein, the CytR repressor. Cell 1993;75:557-566.
61. Spolar RS, Record MT Jr: Coupling of local folding to site-specific binding of proteins to DNA. Science 1994;263:777-784.
62. Tutar Y: Chemical linkage at allosteric activation of Escherichia coli cAMP receptor protein. Protein J 2008a;27:21-29.
63. Tutar Y: Syn, anti, and finally both conformations of cyclic AMP are involved in the CRP-dependent transcription initiation mechanism in Escherichia coli lac operon. Cell Biochem Funct 2008b;26:399-405.
64. Tworzydlo M, Polit A, Mikolajczak J, Wasylewski Z: Fluorescence quenching and kinetic studies of conformational changes induced by DNA and cAMP binding to cAMP receptor protein from Escherichia coli. FEBS J 2005;272:1103-1116.
65. Wasylewski M, Malecki J, Wasylewski Z: Fluorescence study of Escherichia coli cyclic AMP receptor protein. J Protein Chem 1995;14:299-308.
66. Weber IT, Steitz TA: Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5-Å resolution. J Mol Biol 1987;198:311-326.
67. Weyand NJ, Braaten BA, van der Woude M, Tucker J, Low DA: The essential role of the promoter-proximal subunit of CAP in pap phase variation: Lrp - and helical phase-dependent activation of papBA transcription by CAP from-215. Mol Microbiol 2001;39:1504-1522.
68. Won HS, Lee TW, Park SH, Lee BJ: Stoichiometry and structural effect of the cyclic nucleotide binding to cyclic AMP receptor protein. J Biol Chem 2002;277:11450-11455.
69. Won HS, Yamazaki T, Lee TW, Yoon MK, Park SH, Kyogoku Y, Lee BJ: Structural understanding of the allosteric conformational change of cyclic AMP receptor protein by cyclic AMP binding. Biochemistry 2000;39:13953-13962.
70. Zhang X, Ebright R: Identification of a contact between arginine-180 of catabolite gene activator protein (CAP) and base pair 5 of the DNA site in the CAP-DNA complex. Proc Natl Acad Sci USA 1990;87:4717-4721.
71. Zhang X, Schleif R: Catabolite gene activator protein mutations affecting activity of the araBAD promoter. J Bacteriol 1998;180:195-200.
72. Zheng D, Constantinidou C, Hobman JL, Minchin SD: Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res 2004;32:5874-5893.
73. Zhou Y, Merkel TJ, Ebright RH: Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). II. Role at class I and class II CAP-dependent promoters. J Mol Biol 1994;243:603-610.
74. Zubay G, Schwartz D, Beckwith J: Mechanism of activation of catabolite-sensitive genes: a positive control system. Proc Natl Acad Sci USA 1970;66:104-110.