An intersubunit contact stimulating transcription initiation by E. coli RNA polymerase: Interaction of the α C-terminal domain and σ region 4

Genes and Development

Volumn 17, Issue 10, 2003, Pages 1293-1307

  Ross, Wilma ^a   Schneider, David A ^a   Paul, Brian J ^a   Mertens, Aaron ^a   Gourse, Richard L ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

subunit; subunit; Promoter; RNA polymerase; Transcription activation; UP element

Indexed keywords

DEOXYRIBONUCLEASE; DNA; RNA POLYMERASE; TRANSCRIPTION FACTOR;

ALPHA CHAIN; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; DNA SEQUENCE; ESCHERICHIA COLI; MUTATION; NONHUMAN; PRIORITY JOURNAL; THERMUS AQUATICUS; TRANSCRIPTION INITIATION;

AMINO ACID SUBSTITUTION; BINDING SITES; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; PROMOTER REGIONS (GENETICS); TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI; THERMUS; THERMUS AQUATICUS;

EID: 0038522852     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.1079403     Document Type: Article

References (58)

1. Aiyar, S.E., McLeod, S.M., Ross, W., Hirvonen, C.A., Thomas, M.S., Johnson, R.C., and Gourse, R.L. 2002. Architecture of Fis-activated transcription complexes at the Escherichia coli rrnB P1 and rrnE P1 promoters. J. Mol. Biol. 316: 501-516.
2. Barker, M.M., Gaal, T., Josaitis, C.A., and Gourse, R.L. 2001. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J. Mol. Biol. 305: 673-688.
3. Benoff, B., Yang, H., Lawson, C.L., Parkinson, G., Liu, J., Blatter, E., Ebright, Y.W., Berman, H.M., and Ebright, R.H. 2002. Structural basis of transcription activation: The CAP-αCTD-DNA complex. Science 297:1562-1566.
4. 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.
5. Borukhov, S., Sagitov, V., Josaitis, C.A., Gourse, R.L., and Goldfarb, A. 1993. Two modes of transcription initiation at the rrnB P1 promoter of Escherichia coli. J. Biol. Chem. 268: 23477-23482.
6. Burr, T., Mitchell, J., Minchin, S., and Busby, S. 2000. DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: A systmeatic study. Nucleic Acids Res. 28: 1864-1870.
7. Busby, S. and Ebright, R.H. 1999. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293: 199-213.
8. Campbell, E.A., Muzzin, O., Chlenov, M., Sun, J.L., Olson, C.A., Weinman, O., Trester-Zedlitz, M.L., and Darst, S.A. 2002. Structure of the bacterial RNA polymerase promoter specificity σ subunit. Mol. Cell 9: 527-539.
9. Chung, C.T., Niemela, S.L., and Miller, R.H. 1989. One-step preparation of competent Escherichia coli: Transformation and storage of bacterial cells in the same solution. Proc. Natl. Acad. Sci. 86: 2172-2175.
10. 2+ binding and its structural consequences at the transcription start site. Biochemistry 34: 15624-15632.
11. Estrem, S.T., Gaal, T., Ross, W., and Gourse, R.L. 1998. Identification of an UP element consensus sequence for bacterial promoters. Proc. Natl. Acad. Sci. 95: 9761-9766.
12. Estrem, S.T., Ross, W., Gaal, T., Chen, Z.W.S., Niu, W., Ebright, R.H., and Gourse, R.L. 1999. Bacterial promoter architecture: Subsite structure of UP elements and interactions with the C-terminal domain of the RNA polymerase α subunit. Genes & Dev. 13: 2134-2147.
13. Gaal, T., Barkei, J., Dickson, R.R., de Boer, H.A., deHaseth, P.L., Alavi, H., and Gourse, R.L. 1989. Saturation mutagenesis of an E. coli rRNA promoter and initial characterization of promoter variants. J. Bacteriol. 171: 4852-4861.
14. Gaal, T., Ross, W., Blatter, E.E., Tang, H., Jia, X., Krishnan, V.V., Assa-Munt, N., Ebright, R.H., and Gourse, R.L. 1996. DNA-binding determinants of the α subunit of RNA polymerase: Novel DNA-binding domain architecture. Genes & Dev. 10: 16-26.
15. Gaal, T., Bartlett, M.S., Ross, W., Turnbough Jr., C.L., and Gourse, R.L. 1997. Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria. Science 278: 2092-2097.
16. Gourse, R.L. 1988. Visualization and quantitative analysis of complex formation between E. coli RNA polymerase and an rRNA promoter in vitro. Nucleic Acids Res. 16: 9789-9809.
17. Gourse, R.L., Ross, W., and Gaal, T. 2000. UPs and downs in bacterial transcription initiation: Role of the α subunit of RNA polymerase in promoter recognition. Mol. Microbiol. 37: 687-695.
18. Gross, C.A., Chan, C., Dombroski, A., Gruber, T., Sharp, M., Tupy, J., and Young, B. 1998. The functional and regulatory roles of σ factors in transcription. Cold Spring Harb. Symp. Quant. Biol. 63: 141-155.
19. 70-type σ factors of group 1 and group 2. J. Bacteriol. 179: 1734-1747.
20. Hochschild, A. and Dove, S. 1998. Protein-protein contacts that activate and repress prokaryotic transcription. Cell 92: 597-600.
21. Jafri, S., Urbanowski, M.L., and Stauffer, G.V. 1995. A mutation in the rpoA gene encoding the α subunit of RNA polymerase that affects metE-metR transcription in Escherichia coli. J. Bacteriol. 177: 524-529.
22. -. 1996. The glutamic acid residue at amino acid 261 of the α subunit is a determinant of the intrinsic efficiency of RNA polymerase at the mete core promoter in Escherichia coli. J. Bacteriol. 178: 6810-8106.
23. Jeon, Y.H., Negishi, T., Shirakawa, M., Yamazaki, T., Fujita, N., Ishihama, A., and Kyogoku, Y. 1995. Solution structure of the activator contact domain of the RNA polymerase α subunit. Science 270: 1495-1497.
24. Jeon, Y.H., Yamazaki, T., Otomo, T., Ishihama, A., and Kyogoku, Y. 1997. Flexible linker in the RNA polymerase α subunit facilitates the independent motion of the C-terminal activator contact domain. J. Mol. Biol. 267: 953-962.
25. Kainz, M. and Gourse, R.L. 1998. The C-terminal domain of the α subunit of Escherichia coli RNA polymerase is required for efficient rho-dependent transcription termination. J. Mol. Biol. 284: 1379-1390.
26. 70 subunit of Escherichia coli RNA polymerase in transcriptional activation by activator protein PhoB. Mol. Gen. Genet. 248: 1-8.
27. 70 that result in defects in phage σ repressor-stimulated transcription. J. Bacteriol. 176: 2991-2998.
28. 70 subunit of RNA polymerase according to promoter architecture: Identification of the target of Ada activation at the alkA promoter. J. Bactenol. 181: 1524-1529.
29. Li, M., Moyle, H., and Susskind, M.M. 1994. Target of the transcriptional activation function of phage lambda cI protein. Science 263: 75-77.
30. 70 subunit. J. Mol. Biol. 284: 1353-1365.
31. Marr, M.T. and Roberts, J.W. 1997. Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide. Science 276: 1258-1260.
32. McClure, W.R. 1980. Rate-limiting steps in RNA chain initiation. Proc. Natl. Acad. Sci. 77:5634-5638.
33. McLeod, S.M., Aiyar, S.E., Gourse, R.L., and Johnson, R.C. 2002. The C-terminal domains of the RNA polymerase α subunits: Contact site with Fis and localization during co-activation with CRP at the Escherichia coli proP P2 promoter. J. Mol. Biol. 316: 517-529.
34. Murakami, K., Fujita, N., and Ishihama, A. 1996. Transcription factor recognition surface on the RNA polymerase α subunit is involved in contact with the DNA enhancer element. EMBO J. 15: 4358-4367.
35. Murakami, K.S., Masuda, S., and Darst, S.A. 2002a. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Science 296: 1280-1284.
36. Murakami, K.S., Masuda, S., Campbell, E.A., Muzzin, O., and Darst, S.A. 2002b. Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex. Science 296: 1285-1290.
37. Newlands, J.T., Ross, W., Gosink, K.K., and Gourse, R.L. 1991. Factor-independent activation of Escherichia coli rRNA transcription. II. Characterization of complexes of rrnB P1 promoters containing or lacking the upstream activator region with Escherichia coli RNA polymerase. J. Mol. Biol. 220: 569-583.
38. 70 region 4 involved in transcription activation by λ cI. J. Mol. Biol. 324: 17-34.
39. Niu, W., Kim, Y., Tau, G., Heyduk, T., and Ebright, R.H. 1996. Transcription activation at class II CAP-dependent promoters: Two interactions between CAP and RNA polymerase. Cell 87: 1123-1134.
40. 70 subunit of Escherichia coli RNA polymerase. J. Bacteriol. 184: 3957-3964.
41. Rao, L., Ross, W., Appleman, J.A., Gaal, T., Leirmo, S., Schlax, P.J., Record Jr., M.T., and Gourse, R.L. 1994. Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. J. Mol. Biol. 235: 1421-1435.
42. 70 subunit: Application of suppression genetics. J. Mol. Biol. 299: 311-324.
43. R promoter. J. Mol. Biol. 176: 495-522.
44. Ross, W., Thompson, J.F., Newlands, J.T., and Gourse, R.L. 1990. E. coli Fis protein activates rRNA transcription in vitro and in vivo. EMBO J. 9: 3733-3742.
45. Ross, W., Gosink, K.K., Salomon, J., Igarashi, K., Zou, C., Ishihama, A., Severinov, K., and Gourse, R.L. 1993. A third recognition element in bacterial promoters: DNA binding by the α subunit of RNA polymerase. Science 262: 1407-1413.
46. Ross, W., Aiyar, S.E., Salomon, J., and Gourse, R.L. 1998. Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J. Bacteriol. 180:5375-5383.
47. Ross, W., Ernst, A., and Gourse, R.L. 2001. Fine structure of E. coli RNA polymerase-promoter interactions: α Subunit binding to the UP element minor groove. Genes & Dev. 15: 491-506.
48. R promoter: Large scale conformational changes in forming the kinetically significant intermediates. J. Mol. Biol. 319: 649-671.
49. Savery, N.J., Lloyd, G.S., Kainz, M., Gaal, T., Ross, W., Ebright, R.H., Gourse, R.L., and Busby, S.J.W. 1998. Transcription activation at class II CRP-dependent promoters: Identification of determinants in the C-terminal domain of the RNA polymerase α subunit. EMBO J. 17: 3439-3447.
50. Savery, N.J., Lloyd, G.S., Busby, S.J.W., Thomas, M.S., Ebright, R.H., and Gourse R.L. 2002. Determinants of the C-terminal domain of the Escherichia coli RNA polymerase α subunit important for transcription at class I cyclic AMP receptor protein-dependent promoters. J. Bacteriol. 184: 2273-2280.
51. Shao, X. and Grishin, N.V. 2000. Common fold in helix-hairpin-helix proteins. Nucleic Acids Res. 28: 2643-2650.
52. Strainic Jr., M.G., Sullivan, J.J., Velevis, A., and deHaseth, P.L. 1998. Promoter recognition by Escherichia coli RNA polymerase: Effects of the UP element on open complex formation and promoter clearance. Biochemistry 37: 18074-18080.
53. Tang, H., Severinov, K., Goldfarb, A., Fenyo, D., Chait, B., and Ebright, R.H. 1994. Location, structure, and function of the target of a transcriptional activator protein. Genes & Dev. 8: 3058-3067.
54. Tang, H., Kim, Y., Severinov, K., Goldfarb, A., and Ebright, R.H. 1996. Escherichia coli RNA polymerase holoenzyme: Rapid reconstitution from recombinant α, β, β′, and σ subunits. Methods Enzymol. 273: 130-140.
55. 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 A resolution. Nature 417: 712-719.
56. Wada, T., Yamazaki, T., and Kyogoku, Y. 2000. The structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase α subunit from Thermus thermophilus. J. Biol. Chem. 275: 16057-16063.
57. Yang, J., Murakami, K., Camakaris, H., Fujita, N., Ishihama, A., and Pittard, A.J. 1997. Amino acid residues in the α-subunit C-terminal domain of Escherichia coli RNA polymerase involved in activation of transcription from the mtr promoter. J. Bacteriol. 179: 6187-6191.
58. Yasuno, K., Yamazaki, T., Tanaka, Y., Kodama, T.S., Matsugami, A., Katahira, M., Ishihama, A., and Kyogoku, Y. 2001. Interaction of the C-terminal domain of the E. coli RNA polymerase α subunit with the UP element: Recognizing the backbone structure in the minor groove surface. J. Mol. Biol. 306: 213-225.