Dual targets of a transcriptional activator that tracks on DNA

EMBO Journal

Volumn 16, Issue 11, 1997, Pages 3124-3132

  Sanders, Glenn M ^a,b   Kassavetis, George A ^a   Geiduschek, E Peter ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Bacteriophage T4 late genes; DNA tracking proteins; T4 gp33; T4 gp55; Transcriptional regulation

Indexed keywords

BACTERIOPHAGE DNA; DNA POLYMERASE; SIGMA FACTOR; TRANSACTIVATOR PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIOPHAGE T4; CARBOXY TERMINAL SEQUENCE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN TARGETING; TRANSACTIVATION;

BACTERIOPHAGE T4; BINDING SITES; CROSS-LINKING REAGENTS; DNA-DIRECTED DNA POLYMERASE; DNA-DIRECTED RNA POLYMERASES; GENE EXPRESSION REGULATION, VIRAL; PHOTOCHEMISTRY; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; SIGMA FACTOR; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

EID: 0030973043     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.11.3124     Document Type: Article

References (69)

1. Barberis, A., Pearlberg, J., Simkovich, N., Farrell, S., Reinagel, P., Bamdad, C., Sigal, G. and Ptashne, M. (1995) Contact with a component of the polymerase II holoenzyme suffices for gene activation. Cell, 81, 359-368.
2. Bartholomew, B., Tinker, R., Kassavetis, G. and Geiduschek, E.P. (1995) A photocrosslinking assay for DNA-tracking by replication proteins. Methods Enzymol., 262, 476-494.
3. Berdis, A.J., Soumillion, P. and Benkovic, S.J. (1996) The carboxyl terminus of the bacteriophage T4 DNA polymerase is required for holoenzyme complex formation. Proc. Natl Acad. Sci. USA, 93, 12822-12827.
4. Bolle, A., Epstein, R., Salser, W. and Geiduschek, E.P. (1968) Transcription during bacteriophage T4 development: synthesis and relative stability of early and late RNA. J. Mol. Biol., 31, 325-348.
5. Bradford, M.M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem., 72, 248-254.
6. Brody, E., Kassavetis, G., Ouhammouch, M., Sanders, G., Tinker, R. and Geiduschek, E.P. (1995) Old phage, new insights: two recently recognized mechanisms of transcriptional regulation in bacteriophage T4 development. FEMS Microbiol. Lett., 128, 1-8.
7. Busby, S., West, D., Lawes, M., Webster, C., Ishihama, A. and Kolb, A. (1994) Transcription activation by the Escherichia coli cyclic AMP receptor protein. Receptors bound in tandem at promoters can interact synergistically. J. Mol. Biol., 241, 341-352.
8. Chi, T., Lieberman, P., Ellwood, K. and Carey, M. (1995) A general mechanism for transcriptional synergy by eukaryotic activators. Nature, 377, 254-257.
9. Choi, M., Miller, A., Cho, N.Y. and Rothman-Denes, L.B. (1995) Identification, cloning, and characterization of the bacteriophage N4 gene encoding the single-stranded DNA-binding protein. A protein required for phage replication, recombination, and late transcription. J. Biol. Chem., 270, 22541-22547.
10. Coppo, A., Manzi, A. and Pulitzer, J.F. (1975) Host mutant (tabD)-induced inhibition of bacteriophage T4 late transcription. II. Genetic characterization of mutants. J. Mol. Biol., 96, 601-624.
11. Edwards, A.M. and Kane, C.M. (1996) Identifying regulators of transcript elongation in eukaryotes. Methods Enzymol., 274, 419-436.
12. Elliott, T. and Geiduschek, E.P. (1984) Defining a bacteriophage T4 late promoter: absence of a '-35' region. Cell. 36, 211-219.
13. Farrell, S., Simkovich, N., Wu, Y.B., Barberis, A. and Ptashne, M. (1996) Gene activation by recruitment of the RNA polymerase II holoenzyme. Genes Dev., 10, 2359-2367.
14. Geiduschek, E.P., Fu, T.-J., Kassavetis, G.A., Sanders, G.M. and Tinker-Kulberg, R.L. (1997) Transcriptional activation by a topologically linkable protein: forging a connection between replication and gene activity. Nucleic Acids Res. Mol. Biol., 11, 135-150.
15. Hager, D.A. and Burgess, R.R. (1980) Elution of proteins from sodium dodecyl sulfate-polyacrylamide gels, removal of sodium dodecyl sulfate, and renaturation of enzymatic activity: results with sigma subunit of Escherichia coli RNA polymerase, wheat germ DNA topoisomerase, and other enzymes. Anal. Biochem., 109, 76-86.
16. Hawley, D.K. and McClure, W.R. (1982) Mechanism of activation of transcription initiation from the lambda PRM promoter. J. Mol. Biol., 157, 493-525.
17. Herendeen, D.R., Kassavetis, G.A., Barry, J., Alberts, B.M. and Geiduschek, E.P. (1989) Enhancement of bacteriophage T4 late transcription by components of the T4 DNA replication apparatus. Science, 245, 952-958.
18. Herendeen, D.R., Williams, K.P., Kassavetis, G.A. and Geiduschek, E.P. (1990) An RNA polymerase-binding protein that is required for communication between an enhancer and a promoter. Science, 248, 573-578.
19. Herendeen, D.R., Kassavetis, G.A. and Geiduschek, E.P. (1992) A transcriptional enhancer whose function imposes a requirement that proteins track along DNA. Science, 256, 1298-1303.
20. Herschlag, D. and Johnson, B.F. (1993) Synergism in transcriptional activation: a kinetic view. Genes Dev., 7, 173-179.
21. Hori, R. and Carey, M. (1994) The role of activators in assembly of RNA polymerase II transcription complexes. Curr. Opin. Genet. Dev., 4, 236-244.
22. Igarashi, K. and Ishihama, A. (1991) Bipartite functional map of the E.coli RNA polymerase alpha subunit: involvement of the C-terminal region in transcription activation by cAMP-CRP. Cell, 65, 1015-1022.
23. Joung, J.K., Koepp, D.M. and Hochschild, A. (1994) Synergistic activation of transcription by bacteriophage lambda cI protein and E.coli cAMP receptor protein. Science, 265, 1863-1866.
24. Kassavetis, G.A., Elliott, T., Rabussay, D.P. and Geiduschek, E.P. (1983) Initiation of transcription at phage T4 late promoters with purified RNA polymerase. Cell, 33, 887-897.
25. Kelman, Z. and O'Donnell, M. (1995) Structural and functional similarities of prokaryotic and eukaryotic DNA polymerase sliding clamps. Nucleic Acids Res., 23, 3613-3620.
26. Kingston, R.E., Bunker, C.A. and Imbalzano, A.N. (1996) Repression and activation by multiprotein complexes that alter chromatin structure. Genes Dev., 10, 905-920.
27. Kobayashi, N., Boyer, T.G. and Berk, A. (1995) A class of activation domains interacts directly with TFIIA and stimulates TFIIA-TFIID-promoter complex assembly. Mol. Cell. Biol., 15, 6465-6473.
28. Kong, X.P., Onrust, R., O'Donnell, M. and Kuriyan, J. (1992) Three-dimensional structure of the beta subunit of E.coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell, 69, 425-437.
29. Krishna, T.S., Kong, X.-P., Gary, S., Burgers, P.M. and Kuriyan, J. (1994) Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell, 79, 1233-1243.
30. Krude, T. and Elgin, S.C.R. (1996) Chromatin: pushing nucleosomes around. Curr. Biol., 6, 511-515.
31. Li, M., Moyle, H. and Susskind, M.M. (1994) Target of the transcriptional activation function of phage lambda cI protein. Science, 263, 75-77.
32. Li, M., McClure, W.R. and Susskind, M.M. (1997) Changing the mechanism of transcriptional activation by phage lambda repressor. Proc. Natl Acad. Sci. USA, 94, 3691-3696.
33. Lieberman, P.M. and Berk, A.J. (1994) A mechanism for TAFs in transcriptional activation: activation domain enhancement of TFIID-TFIIA-promoter DNA complex formation. Genes Dev., 8, 995-1006.
34. Malan, T.P., Kolb, A., Buc, H. and McClure, W.R. (1984) Mechanism of CRP-cAMP activation of lac operon transcription initiation activation of the P1 promoter. J. Mol. Biol., 180, 881-909.
35. Maldonado, E. and Reinberg, D. (1995) News on initiation and elongation of transcription by RNA polymerase II. Curr. Opin. Cell Biol., 7, 352-361.
36. Malik, S. and Goldfarb, A. (1988) Late sigma factor of bacteriophage T4. Formation and properties of RNA polymerase-promoter complexes. J. Biol. Chem., 263, 1174-1181.
37. McClure, W.R. (1985) Mechanism and control of transcription initiation in prokaryotes. Annu. Rev. Biochem., 54, 171-204.
38. Monsalve, M., Mencia, M., Salas, M. and Rojo, F. (1996) Protein P4 represses phage φ29 A2C promoter by interaction with the α subunit of Bacillus subtilis RNA polymerase. Proc. Natl Acad. Sci. USA, 93, 8913-8918.
39. Ptashne, M. and Gann, A.A. (1990) Activators and targets. Nature, 346, 329-331.
40. Rasmussen, E.B. and Lis, J.T. (1995) Short transcripts of the ternary complex provide insight into RNA polymerase II elongational pausing. J. Mol. Biol., 252, 522-535.
41. 70), promoters, and the kinetics of the steps of transcription initiation. In Neidhardt, F.C. (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. American Society of Microbiology, Washington, DC, pp. 792-820.
42. Reddy, M.K., Weitzel, S.E. and von Hippel, P.H. (1993) Assembly of a functional replication complex without ATP hydrolysis: a direct interaction of bacteriophage T4 gp45 with T4 DNA polymerase. Proc. Natl Acad. Sci. USA, 90, 3211-3215
43. 70 in promoter-proximal pausing. Cell. 86, 485-493.
44. Riva, S., Cascino, A. and Geiduschek, E.P. (1970) Coupling of late transcription to viral replication in bacteriophage T4 development. J. Mol. Biol., 54, 85-102.
45. Sanders, G.M. (1996) Activation of transcription by a DNA-tracking protein. PhD Thesis, University of California, San Diego
46. Sanders, G.M., Kassavetis, G.A. and Geiduschek, E.P. (1994) Use of a macromolecular crowding agent to dissect interactions and define functions in transcriptional activation by a DNA-tracking protein: bacteriophage T4 gp45 and late transcription. Proc. Natl Acad. Sci. USA, 91, 7703-7707.
47. Sanders, G.M., Kassavetis, G.A. and Geiduschek, E.P. (1995) Rules governing the efficiency and polarity of loading a tracking clamp protein onto DNA: determinants of enhancement in bacteriophage T4 late transcription. EMBO J., 14, 3966-3976.
48. Sauer, F., Hansen, S.K. and Tjian, R. (1995) Multiple TAFIIs directing synergistic activation of transcription. Science, 270, 1783-1788.
49. Schagger, H. and von Jagow, G. (1987) Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal. Biochem., 166, 368-379.
50. Shih, M.C. and Gussin, G.N. (1983) Differential effects of mutations on discrete steps in transcription initiation at the lambda PRE promoter. Cell, 34, 941-949.
51. Stargell, L.A. and Struhl, K. (1996a) Mechanisms of transcriptional activation in vivo: two steps forward. Trends Genet., 12, 311-315.
52. Stargell, L.A. and Struhl, K. (1996b) A new class of activation-defective TATA-binding protein mutants: evidence for two steps of transcriptional activation in vivo. Mol. Cell. Biol., 16, 4456-4464.
53. Struhl, K. (1995) Yeast transcriptional regulatory mechanisms. Annu. Rev. Genet., 29, 651-674.
54. Struhl, K. (1996) Chromatin structure and RNA polymerase II connection: implications for transcription. Cell, 84, 179-182.
55. Studier, F.W. and Moffatt, B.A. (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol., 189, 113-130.
56. Svären, J. and Hörz, W. (1996) Regulation of gene expression by nucleosomes. Curr. Opin. Genet. Dev., 6, 164-170.
57. Tanaka, M. (1996) Modulation of promoter occupancy by cooperative DNA binding and activation-domain function is a major determinant of transcriptional regulation by activators in vivo. Proc. Natl Acad. Sci. USA, 93, 4311-4315.
58. Tinker, R.L., Williams, K.R., Kassavetis, G.A. and Geiduschek, E.P. (1994a) Transcriptional activation by a DNA-tracking protein: structural consequences of enhancement at the T4 late promoter. Cell, 77, 225-237.
59. Tinker, R.L, Kassavetis, G.A. and Geiduschek, E.P. (1994b) Detecting the ability of viral, bacterial and eukaryotic replication proteins to track along DNA. EMBO J., 13, 5330-5337.
60. Tinker, R.L., Sanders, G.M., Severinov, K., Kassavetis, G.A. and Geiduschek, E.P. (1995) The C-termmal domain of the RNA polymerase α subunit in transcriptional enhancement and deactivation at the bacteriophage T4 late promoter. J. Biol. Chem., 270, 15899-15907.
61. Tinker-Kulberg, R.L., Fu, T.-J., Geiduschek, E.P., and Kassavetis, G.A. (1996) A direct interaction between a DNA-tracking protein and a promoter-recognition protein: implications for searching DNA sequence. EMBO J., 15, 5032-5039.
62. Tjian, R. and Maniatis, T. (1994) Transcriptional activation: a complex puzzle with few easy pieces. Cell, 77, 5-8.
63. Triezenberg, S.J. (1995) Structure and function of transcriptional activation domains. Curr. Opin. Genet. Dev., 5, 190-196.
64. Williams, K.P., Kassavetis, G.A. and Geiduschek, E.P. (1987) Interactions of the bacteriophage T4 gene 55 product with Escherichia coli RNA polymerase. Competition with Escherichia coli sigma 70 and release from late T4 transcription complexes following initiation. J. Biol. Chem., 262, 12365-12371.
65. Williams, K.P., Müller, R., Rüger, W. and Geiduschek, E.P. (1989) Overproduced bacteriophage T4 gene 33 protein binds RNA polymerase. J. Bacteriol., 171, 3579-3582.
66. Wilson, C.J., Chao, D.M., Imbalzano, A.N., Schnitzler, G.R., Kingston, R.E. and Young, R.A. (1996) RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell, 84, 235-244.
67. Winkelman, J.W., Kassavetis, G.A. and Geiduschek, E.P. (1994) Molecular genetic analysis of a prokaryotic transcriptional coactivator: functional domains of the bacteriophage T4 gene 33 protein. J. Bacteriol., 176, 1164-1171.
68. Wolffe, A.P. and Pruss, D. (1996) Targeting chromatin disruption: transcription regulators that acetylate histones. Cell, 84, 817-819.
69. Xiao, H. et al. (1994) Binding of basal transcription factor TFIIH to the acidic activation domains of VP16 and p53. Mol. Cell. Biol., 14, 7013-7024.