Region 4 of σ as a target for transcription regulation

Molecular Microbiology

Volumn 48, Issue 4, 2003, Pages 863-874

  Dove, Simon L ^a   Darst, Seth A ^b   Hochschild, Ann ^c  

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b ROCKEFELLER UNIVERSITY   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; BACTERIAL RNA; DNA BINDING PROTEIN; PROTEIN MOTA; PROTEIN RHAS; RNA POLYMERASE; SIGMA FACTOR; UNCLASSIFIED DRUG;

BACTERIOPHAGE LAMBDA; DNA PROTEIN COMPLEX; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; RNA TRANSLATION; SHORT SURVEY; THERMUS AQUATICUS; THERMUS THERMOPHILUS; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

BACTERIOPHAGE LAMBDA; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; SIGMA FACTOR; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); BACTERIOPHAGE LAMBDA; ESCHERICHIA COLI; NEGIBACTERIA; THERMUS AQUATICUS; THERMUS THERMOPHILUS;

EID: 0038354921     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.2003.03467.x     Document Type: Short Survey

References (75)

1. 70 subunit of Escherichia coli RNA polymerase. J Biol Chem 272: 27435-27433.
2. Alper, S., Duncan, L., and Losick, R. (1994) An adenosine nucleotide switch controlling the activity of a cell type-specific transcription factor in B. subtilis. Cell 77: 195-205.
3. 70 binding site on the N terminus of the Escherichia coli RNA polymerase β' subunit. J Biol Chem 273: 31381-31387.
4. 70 subunits of Escherichia coli RNA polymerase. J Biol Chem 271: 32343-32348.
5. 70-retaining transcription elongation complexes from Escherichia coli. Cell 106: 443-451.
6. Bhende, P.M., and Egan, S.M. (2000) Genetic evidence that transcription activation by RhaS involves specific amino acid contacts with sigma 70. J Bacteriol 182: 4959-4969.
7. Bown, J.A., Barne, K.A., Minchin, S.D., and Busby, S.J.W. (1997) Extended - 10 promoters. Nucleic Acids Mol Biol 11: 41-52.
8. Burgess, R.R., Travers, A.A., Dunn, J.J., and Bautz, E.K. (1969) Factor stimulating transcription by RNA polymerase. Nature 221: 43-46.
9. Busby, S., and Ebright, R.H. (1997) Transcription activation at class II CAP-dependent promoters. Mol Microbiol 23: 853-859.
10. Busby, S., and Ebright, R.H. (1999) Transcription activation by catabolite activator protein (CAP). J Mol Biol 293: 199-213.
11. Bushman, F.D., Shang, C., and Ptashne, M. (1989) A single glutamic acid residue plays a key role in the transcriptional activation function of lambda repressor. Cell 58: 1163-1171.
12. 70 subunit. Mol Cell 3: 229-238.
13. Campbell, E.A., Muzzin, O., Chlenov, M., Sun, J.L., Olson, C.A., Weinman, O., et al. (2002a) Structure of the bacterial RNA polymerase promoter specificity σ subunit. Mol Cell 9: 527-539.
14. F. Cell 108: 795-807.
15. 28 holoenzyme destabilization through stepwise binding. J Mol Biol 306: 915-929.
16. 28 RNA polymerase holoenzyme. Genes Dev 12: 3123-3136.
17. Colland, F., Orsini, G., Brody, E.N., Buc, H., and Kolb, A. (1998) The bacteriophage T4 AsiA protein: a molecular switch for sigma 70-dependent promoters. Mol Microbiol 27: 819-829.
18. 28 factor. Mol Microbiol 41: 477-487.
19. F and its antisigma factor SpollAB. Genes Dev 10: 2348-2358.
20. F of Bacillus subtilis. Genes Dev 8: 2653-2663.
21. 70 exhibit specificity of binding to promoter DNA. Cell 70: 501-512.
22. Dove, S.L., Huang, F.W., and Hochschild, A. (2000) Mechanism for a transcriptional activator that works at the isomerization step. Proc Natl Acad Sci USA 97: 13215-13220.
23. F from Bacillus subtilis. Proc Natl Acad Sci USA 90: 2325-2329.
24. F from its anti-sigma factor SpollAB. J Mol Biol 260: 147-164.
25. Ebright, R.H., and Busby, S. (1995) The Escherichia coli RNA polymerase α subunit: structure and function. Curr Opin Genet Dev 5: 197-203.
26. 70 subunit of RNA polymerase with altered promoter specificity. J Mol Biol 206: 579-590.
27. Gourse, R.L., Ross, W., and Gaal, T. (2000) UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol Microbiol 37: 687-695.
28. Gross, C.A., Chan, C., Dombroski, A., Gruber, T., Sharp, M., Tupy, J., and Young, B. (1998) The functional and regulatory roles of sigma factors in transcription. Cold Spring Harb Symp Quant Biol 63: 141-155.
29. Helmann, J.D. (1999) Anti-sigma factors. Curr Opin Microbiol 2: 135-141.
30. 70. J Mol Biol 304: 731-739.
31. Hochschild, A., and Dove, S.L. (1998) Protein-protein contacts that activate and repress prokaryotic transcription. Cell 92: 597-600.
32. Hochschild, A., Irwin, N., and Ptashne, M. (1983) Repressor structure and the mechanism of positive control. Cell 32: 319-325.
33. Hughes, K.T., and Mathee, K. (1998) The anti-sigma factors. Annu Rev Microbiol 52: 231-286.
34. Ishihama, A. (2000) Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol 54: 499-518.
35. Jishage, M., and Ishihama, A. (1998) A stationary phase protein in Escherichia coli with binding activity to the major σ subunit of RNA polymerase. Proc Natl Acad Sci USA 95: 4953-4958.
36. Kenney, T.J., and Moran, C.P.J. (1991) Genetic evidence for interaction of sigmaA with two promoters in Bacillus subtilis. J Bacteriol 173: 3282-3290.
37. 70 that result in defects in phage λ repressor-stimulated transcription. J Bacteriol 176: 2991-2998.
38. Kutsukake, K., Iyoda, S., Shnishi, K., and Iino, T. (1994) Genetic and molecular analyses of the interaction between the flagellum-specific sigma and anti-sigma factors in Salmonella typhimurium. EMBO J 13: 4568-4576.
39. Kuznedelov, K., Minakhin, L., Niedziela-Majka, A., Dove, S.L., Rogulja, D., Nickels, B.E., et al. (2002) A role for interaction of the RNA polymerase flap domain with the s subunit in promoter recognition. Science 295: 855-857.
40. Lambert, L.J., Schirf, V., Demeler, B., Cadene, M., and Werner, M.H. (2001) Flipping a genetic switch by subunit exchange. EMBO J 20: 7149-7159.
41. 70 subunit of RNA polymerase according to promoter architecture: identification of the target of Ada activation at the alkA promoter. J Bacteriol 181: 1524-1529.
42. Li, M., Moyle, H., and Susskind, M.M. (1994) Target of the transcriptional activation function of phage λ cl protein. Science 263: 75-77.
43. 70 family: sequence conservation and evolutionary relationships. J Bacteriol 174: 3843-3849.
44. 70 subunit. J Mol Biol 284: 1353-1365.
45. F activity in sporulating Bacillus subtilis. J Bacteriol 179: 3922-3927.
46. Mahren, S., Enz, S., and Braun, V. (2002) Functional interaction of region 4 of the extracytoplasmic function sigma factor Fecl with the cytoplasmic portion of the FecR transmembrane protein of the Escherichia coli ferric citrate transport system. J Bacteriol 184: 3704-3711.
47. 70 subunit of RNA polymerase in transcriptional activation by activator protein PhoB in Escherichia coli. Genes Dev 7: 149-160.
48. Mekler, V., Kortkhonjia, E., Mukhopadhyay, J., Knight, J., Revyakin, A., Kapanidis, A.N., et al. (2002) Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell 108: 599-614.
49. F, the first compartment-specific transcription factor of B. subtilis, is regulated by an anti-sigma factor that is also a protein kinase. Cell 74: 735-742.
50. 70 subunit of E. coli RNA polymerase and T4 AsiA. J Mol Biol 306: 631-642.
51. 70 with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell 106: 453-463.
52. Murakami, K.S., Masuda, S., Campbell, E.A., Muzzin, O., and Darst, S.A. (2002a) Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 296: 1285-1290.
53. Murakami, K.S., Masuda, S., and Darst, S.A. (2002b) Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science 296: 1280-1284.
54. 70 region 4 involved in transcription activation by λcl. J Mol Biol 324: 17-34.
55. 70 subunit of RNA polymerase is contacted by the λQ antiterminator during early elongation. Mol Cell 10: 611-622.
56. 70 subunits participate in transcription of the Escherichia coli uhpT promoter. J Bacteriol 181: 7266-7273.
57. 70 subunit of Escherichia coli RNA polymerase. J Bacteriol 184: 3957-3964.
58. Ptashne, M. (1992) A Genetic Switch, Phage Lambda and Higher Organisms. Cambridge: Cell Press.
59. Rain, J.-C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., et al. (2001) The protein-protein interaction map of Helicobacter pylori. Nature 409: 665-668.
60. Rhee, S., Martin, R.G., Rosner, J.L., and Davies, D.R. (1998) A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator. Proc Natl Acad Sci USA 95: 10413-10418.
61. 70 subunit: application of suppression genetics. J Mol Biol 299: 311-324.
62. Rhodius, V.A., and Busby, S.J.W. (2000b) Transcription activation by the Escherichia coli cyclic AMP receptor protein: determinants within activating region 3. J Mol Biol 299: 295-310.
63. 70 in promoter-proximal pausing. Cell 86: 485-493.
64. Roberts, C.W., and Roberts, J.W. (1996) Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell 86: 495-501.
65. Roberts, J.W., Yarnell, W., Bartlett, E., Guo, J., Marr, M., Ko, D.C., et al. (1998) Antitermination by bacteriophage λ Q protein. Cold Spring Harb Symp Quant Biol 63: 319-325.
66. Severinov, K., and Muir, T.W. (1998) Expressed protein ligation, a novel method for studying protein-protein interactions in transcription. J Biol Chem 273: 16205-16209.
67. 70 subunit. J Mol Biol 263: 637-647.
68. Severinova, E., Severinov, K., and Darst, S.A. (1998) Inhibition of Escherichia coli RNA polymerase by bacteriophage T4 AsiA. J Mol Biol 279: 9-18.
69. 70 subunit of Escherichia coli RNA polymerase. J Mol Biol 206: 591-603.
70. Stitt, B., and Hinton, D. (1994) Regulation of middle-mode transcription. In Molecular Biology of Bacteriophage T4. Karam, J., et al. (eds). Washington, DC: American Society for Microbiology Press, pp. 142-160.
71. E with the RseA anti-sigma factor. J Biol Chem 277: 27282-27287.
72. 70 constitute the recognition sites for the anti-σ factor AsiA, and Asia is a dimer free in solution. J Biol Chem 276: 41128-41132.
73. Urbauer, J.L., Simeonov, M.F., Urbauer, R.J.B., Adelman, K., Gilmore, J.M., and Brody, E.N. (2002) Solution structure and stability of the anti-sigma factor AsiA: implications for novel functions. Proc Natl Acad Sci USA 99: 1831-1835.
74. Vassylyev, D.G., Sekine, S., Laptenko, O., Lee, J., Vassylyeva, M.N., Borukhov, S., and Yokoyama, S. (2002) Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417: 712-719.
75. 70. Cell 105: 935-944.