Interaction of the bacteriophage Mu transcriptional activator protein, C, with its target site in the mom promoter

Journal of Molecular Biology

Volumn 273, Issue 4, 1997, Pages 765-774

  Sun, Weiyong ^a   Hattman, Stanley ^a   Kool, Eric ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

Author keywords

C protein DNA interaction; Chemical protection and interference analysis; Mutagenesis; Phage Mu late promoters; Transcriptional activation

Indexed keywords

DNA BINDING PROTEIN; PROTEIN C; TRANSCRIPTION FACTOR;

ARTICLE; BACTERIOPHAGE MU; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DNA METHYLATION; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA INTERACTION; TRANSACTIVATION; TRANSCRIPTION INITIATION;

ENTEROBACTERIA PHAGE MU;

EID: 0031558775     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1349     Document Type: Editorial

References (53)

1. midentifies a new region required for promoter function. Nucl. Acids Res. 24:1996;450-457.
2. Balke V., Nagaraja V., Gindlesperger T., Hattman S. Functionally distinct RNA polymerase binding sites in the phage Mumom. Nucl. Acids Res. 20:1992;2777-2784.
3. Bölker M., Kahmann R. TheEscherichia colimom. EMBO J. 8:1989;2403-2410.
4. Bölker M., Wulczyn F. G., Kahmann R. Role of bacteriophage Mu C protein in activation of themom. J. Bacteriol. 171:1989;2019-2027.
5. Cabot, T. L. 1995, Transcriptional activation of the bacteriophage Mumom, University of Rochester, Rochester, NY.
6. Chang A. C. Y., Cohen S. N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134:1978;1141-1156.
7. 2. Nucl. Acids Res. 19:1991;5507-5513.
8. Chiang L. W., Howe M. M. Mutational analysis of a C-dependent late promoter of bacteriophage Mu. Genetics. 135:1993;619-629.
9. Churchill M. E. A., Suzuki M. "SPKK' motifs prefer to bind to DNA at A/T-rich sites. EMBO J. 8:1989;4189-4195.
10. Diekmann S., von Kitzing E., McLaughlin L., Ott J., Eckstein F. The influence of exocyclic substituents of purine bases on DNA curvature. Proc. Natl Acad. Sci. USA. 84:1987;8257-8261.
11. Dixon W. J., Hayes J. J., Levin J. R., Weidner M. F., Dombroski B. A., Tullius T. D. Hydroxyl radical footprinting. Methods Enzymol. 208:1991;380-413.
12. Gait M. J., Sproat B. S. Oligonucleotide Synthesis. 1984;IRL Press, Oxford and Washington.
13. Gindlesperger T. C., Hattman S. In vitromom. J. Bacteriol. 176:1994;2885-2891.
14. Gottlieb P. A., Wu S., Zhang X., Tecklenburg M., Kuempel P., Hill T. M. Equilibrium, kinetic, and footprinting studies of the Tus-Ter. J. Biol. Chem. 267:1992;7434-7443.
15. Hattman S., Ives J., Margolin W., Howe M. M. Regulation and expression of the bacteriophage MumomC. Gene. 39:1985;71-76.
16. Hayes J. J., Tullius T. D. The missing nucleoside experiment: a new technique to study recognition of DNA by protein. Biochemistry. 28:1989;9521-9527.
17. Hughes K. T., Gaines P. C. W., Karlinsey J. E., Vinayak R., Simon M. I. Sequence-specific interaction of theSalmonella. EMBO J. 11:1992;2695-2705.
18. Jordan S. R., Pabo C. O. Structure of the lambda complex at 2.5 Å resolution: details of the repressor-operator interactions. Science. 242:1988;893-899.
19. Kahmann R. Themom. Curr. Top. Microbiol. Immunol. 108:1984;29-47.
20. Kim J., Zwieb C., Wu C., Adhya S. Bending of DNA by gene-regulatory proteins: construction and use of a DNA bending vector. Gene. 85:1989;15-23.
21. Kunkel T. A., Roberts J. D., Zakour R. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154:1987;367-382.
22. Lane D., Prentki P., Chandler M. Use of gel retardation to analyze protein-nucleic acid interactions. Microbiol. Rev. 56:1992;509-528.
23. Li T., Ho H. H., Maslak M., Schick C., Martin C. T. Major groove recognition elements in the middle of the T7 RNA polymerase promoter. Biochemistry. 35:1996;3722-3727.
24. Makino K., Amemura M., Kawamoto T., Kimura S., Shinagawa H., Nakata A., Suzuki M. DNA binding of PhoB and its interaction with RNA polymerase. J. Mol. Biol. 259:1996;15-26.
25. Margolin W., Rao G., Howe M. M. Bacteriophage Mu late promoters: four transcripts initiate near a conserved sequence. J. Bacteriol. 171:1989;2003-2018.
26. Mathee K., Howe M. M. Identification of a positive regulator of the Mu middle operon. J. Bacteriol. 172:1990;6641-6650.
27. 70. J. Bacteriol. 175:1993;5314-5323.
28. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc. Natl Acad. Sci. USA. 74:1977;560-564.
29. McBryant S. J., Gedulin B., Clemens K. R., Wright P. E., Gottesfeld J. M. Assessment of major groove and minor groove DNA interactions by zinc fingers ofXenopus. Nucl. Acids Res. 24:1996;2567-2574.
30. Niland P., Hühne R., Müller-Hill B. How AraC interacts specifically with its target DNAs. J. Mol. Biol. 264:1996;667-674.
31. Nordlund T. M., Anderson S., Nilsson L., Rigler R., Graslund A., MaLaughlin L. M. Structure and dynamics of a fluorescent DNA oligomer containing theEco. Biochemistry. 28:1989;9095-9103.
32. Papavassiliou A. G. Chemical nucleases as probes for studying DNA-protein interactions. Biochem. J. 305:1995;345-357.
33. Ramesh V., Nagaraja V. Sequence-specific DNA binding of the phage Mu C protein: footprinting analysis reveals altered DNA conformation upon protein binding. J. Mol. Biol. 260:1996;22-33.
34. Renbaum P., Razin A. Footprint analysis of M.SssHha. J. Mol. Biol. 248:1995;19-26.
35. Schneider B., Ginell S., Jones R., Gaffney B., Berman H. M. Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers. Biochemistry. 31:1992;9622-9628.
36. 666. Nucl. Acids Res. 20:1992;2297-2306.
37. Sowers L. C., Fazakerley G. V., Eritja R., Kaplan B. E., Goodman M. F. Base pairing and mutagenesis: observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR. Proc. Natl Acad. Sci. USA. 83:1986;5434-5438.
38. Starr D. B., Hawley D. K. TFIID binds in the minor groove of the TATA box. Cell. 67:1991;1231-1240.
39. Sun W., Hattman S. Escherichia colimom. Nucl. Acids Res. 24:1996;4042-4049.
40. Swinton D., Hattman S., Crain P. F., Cheng C. S., Smith D. L., McCloskey J. A. Purification and characterization of the unusual deoxynucleoside, α-N-(9-β-D-2′-deoxyribofuranosylpurin-6-yl)glycinamide, specified by the phage Mu modification function. Proc. Natl Acad. Sci. USA. 80:1983;7400-7404.
41. Szatmari G. B., Lapointe M., DuBow M. S. The right end of transposable bacteriophage D108 contains a 520 base pair protein-encoding sequence not present in bacteriophage Mu. Nucl. Acids Res. 15:1987;6691-6704.
42. Thompson J. F., Landy A. Empirical estimation of protein-induced bending angles: applications to λ site-specific recombination complexes. Nucl. Acids Res. 16:1988;9687-9705.
43. Toussaint A. The DNA modification function of temperate phage Mu-1. Virology. 70:1976;17-27.
44. Tullius T. D. Chemical 'snapshots' of DNA: using the hydroxyl radical to study the structure of DNA and DNA-protein complexes. Trends Biochem. Sci. 12:1987;297-300.
45. Tullius T. D. DNA footprinting with hydroxyl radical. Nature. 332:1988;663-664.
46. Tullius T. D., Dombroski B. A. Hydroxyl radical "footprinting": high-resolution information about DNA-protein contacts and application to λ repressor and Cro protein. Proc. Natl Acad. Sci. USA. 83:1986;5469-5473.
47. Tullius T. D., Dombroski B. A., Churchill M. E. A., Kam L. Hydroxyl radical footprinting: a high resolution method for mapping protein-DNA contacts. Methods Enzymol. 155:1987;537-558.
48. Vison C. R., Sigler P. B., McKnight S. L. Scissors-grip model for DNA recognition by a family of leucine zipper proteins. Science. 246:1989;911-916.
49. Waldburger C. W., Sauer R. T. Domains of Mnt repressor: roles in tetramer formation, protein stability, and operator DNA binding. Biochemistry. 34:1995;13109-13116.
50. Wang S., Cosstick R., Gardner J. F., Gumport R. I. The specific binding ofEscherichia coli. Biochemistry. 34:1995;13082-13090.
51. Wu H.-M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 308:1984;509-513.
52. Wu L., Vertino A., Koudelka G. B. Non-contacted bases affect the affinity of synthetic P22 operators for P22 repressor. J. Biol. Chem. 267:1992;9134-9139.
53. Yang C., Nash H. A. The interaction ofE. coli. Cell. 57:1989;869-880.