UPs and downs in bacterial transcription initiation: The role of the alpha subunit of RNA polymerase in promoter recognition

Molecular Microbiology

Volumn 37, Issue 4, 2000, Pages 687-695

  Gourse, Richard L ^a   Ross, Wilma ^a   Gaal, Tamas ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; DNA BINDING PROTEIN; RNA POLYMERASE; TRANSCRIPTION FACTOR;

BACTERIAL GENETICS; BINDING SITE; DNA SEQUENCE; ENZYME SUBUNIT; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; REVIEW; TRANSCRIPTION INITIATION;

BACTERIA; DNA-DIRECTED RNA POLYMERASES; PROMOTER REGIONS (GENETICS); TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0033852409     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.2000.01972.x     Document Type: Review

References (57)

1. Aiyar, S.E., Gourse, R.L., and Ross, W. (1998) Upstream A-tracts increase prokaryotic promoter activity through interactions with the RNA polymerase alpha subunit. Proc Natl Acad Sci USA 95: 14652-14657.
2. Banner, C.D., Moran, C.P. Jr and Losick, R. (1983) Deletion analysis of a complex promoter for a developmentally regulated gene from Bacillus subtilis. J Mol Biol 168: 351-365.
3. Belyaeva, T., Rhodius, V., Webster, C., and Busby, S. (1998) Transcription activation at promoters carrying tandem DNA sites for the Escherichia coli cyclic AMP receptor protein: organiization of the RNA polymerase α subunits. J Mol Biol 277: 789-804.
4. 54-RNA polymerase to the Pu promoter of Pseudomonas putida: role of IHF and αCTD. EMBO J 17: 5120-5128.
5. Blatter, E.E., Ross, W., Tang, H., Gourse, R.L., and Ebright, R.H. (1994) Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 78: 889-896.
6. Bokal, A.J., Ross, W., and Gourse, R.L. (1995) The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter. J Mol Biol 245: 197-207.
7. Bracco, L., Kotlarz, D., Kolb, A., Diekmann, S., and Buc, H. (1989) Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO J 8: 4289-4296.
8. Bujard, H., Brunner, M., Deuschle, U., Kammerer, W., and Knaus, R. (1987) Structure-function relationship of Escherichia coli promoters. In RNA Polymerase and the Regulation of Transcription. Reznikoff, W.S., Burgess, R., Dahlberg, J.E., Gross, C., Record, M.T., Jr, and Wickens, M.P. (eds). New York: Elsevier, pp. 95-103.
9. Burgess, R.R., Travers, A.A., Dunn, J.J., and Bautz, E.K. (1969) Factor stimulating transcription by RNA polymerase. Nature 221: 43-46.
10. Busby, S., and Ebright, R.H. (1994) Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79: 743-746.
11. Busby, S., and Ebright, R.H. (1999) Transcription activation by catabolite activator protein (CAP). J Mol Biol 293: 199-213.
12. Busby, S., Spassky, A., and Chan, B. (1987) RNA polymerase makes important contacts upstream of base pair -49 at the Escherichia coli galactose operon P1 promoter. Gene 53: 145-152.
13. Ellinger, T., Behnke, D., Knaus, R., Bujard, H., and Gralla, J.D. (1994) Context-dependent effects of upstream A-tracts: stimulation or inhibition of Escherichia coli promoter function. J Mol Biol 239: 466-475.
14. 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 USA 95: 9761-9766.
15. Estrem, S.T., Ross, W., Gaal, T., Chen, Z.W.S., Niu, W., Ebright, R.H., et al. (1999) Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase α subunit. Genes Dev 13: 2134-2147.
16. Fredrick, K., Caramori, T., Chen, Y.F., Galizzi, A., and Helmann, J.D. (1995) Promoter architecture in the flagellar regulon of Bacillus subtilis: high-level expression of flagellin by the sigma D RNA polymerase requires an upstream promoter element. Proc Natl Acad Sci USA 92: 2582-2586.
17. Gaal, T., Rao, L., Estrem, S.T., Yang, J., Wartell, R.M., and Gourse, R.L. (1994) Localization of the intrinsically bent DNA region upstream of the E.coli rrnB P1 promoter. Nucleic Acids Res 22: 2344-2550.
18. Gaal, T., Ross, W., Blatter, E.E., Tang, H., Jia, X., Krishnan, V.V., et al. (1996) DNA-binding determinants of the alpha subunit of RNA polymerase: novel DNA-binding domain architecture. Genes Dev 10: 16-26.
19. Galas, D.J., Eggert, M., and Waterman, M.S. (1985) Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. J Mol Biol 186: 117-128.
20. Gartenberg, M.R., and Crothers, D.M. (1990) Synthetic DNA bending sequences increase the rate of in vitro transcription initiation at the Escherichia coli lac promoter. J Mol Biol 219: 217-230.
21. 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.
22. Graves, M.C., and Rabinowitz, J.C. (1986) In vivo and in vitro transcription of the Clostridium pasteurianum ferredoxin gene. Evidence for 'extended' promoter elements in gram positive organisms. J Biol Chem 261: 11409-11415.
23. A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res 23: 2351-2360.
24. Hochschild, A., and Dove, S.L. (1998) Protein-protein contacts that activate and repress prokaryotic transcription. Cell 92: 597-600.
25. 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.
26. Jafri, S., Urbanowski, M.L., and Stauffer, G.V. (1995) A mutation in the rpoA gene encoding the a subunit of RNA polymerase that affects metE-metR transcription in Escherichia coli. J Bacteriol 177: 524-529.
27. Jeon, Y.H., Negishi, T., Shirakawa, M., Yamazaki, T., Fujita, N., Ishihama, A., et al. (1995) Solution structure of the activator contact domain of the RNA polymerase alpha subunit. Science 270: 1495-1497.
28. Jeon, Y.H., Yamazaki, T., Otomo, T., Ishihama, A., and Kyogoku, Y. (1997) Flexible linker in the RNA polymerase alpha subunit facilitates the independent motion of the C-terminal activator contact domain. J Mol Biol 267: 953-962.
29. Johnson, W.C., Moran, C.P. Jr, Banner, C., Zuber, P., and Losick, R. (1983) Anatomy of a complex procaryotic promoter under developmental regulation. In Gene Expression. Hamer, D.H., and Rosenberg, M. (eds). New York: Alan R. Liss, pp. 235-247.
30. Kolb, A., Igarashi, K., Ishihama, A., Lavigne, M., Buckle, M., and Buc, H. (1993) E. coli RNA polymerase deleted in the C-terminal part of its α-subunit, interacts differently with the cAMP-CRP complex at the lacP1 and galP1 promoter. Nucleic Acids Res 21: 319-326.
31. Koo, H.S., Wu, H.M., and Crothers, D.M. (1986) DNA bending at adenine-thymine tracts. Nature 320: 501-506.
32. 70 that result in defects in phage λ repressor-stimulated transcription. J Bacteriol 176: 2991-2998.
33. Leirmo, S., and Gourse, R.L. (1991) Factor-independent activation of Escherichia coli rRNA transcription. I. Kinetic analysis of the roles of the upstream activator region and supercoiling on transcription of the rrnB P1 promoter in vitro. J Mol Biol 220: 555-568.
34. 70 subunit. J Mol Biol 284: 1353-1365.
35. McAllister, C.F., and Achberger, E.C. (1988) Effect of polyadenine-containing curved DNA on promoter utilization in Bacillus subtilis. J Biol Chem 263: 11743-11749.
36. McMahan, S.A., and Burgess, R.R. (1994) Use of aryl azide cross-linkers to investigate protein-protein interactions: an optimization of important conditions as applied to Escherichia coli RNA polymerase and localization of a sigma 70-alpha cross-link to the C-terminal region of alpha. Biochemistry 33: 12092-12099.
37. Mooney, R.A., and Landick, R. (1999) RNA polymerase unveiled. Cell 98: 687-690.
38. Moran, C.P., Jr, Lang, N., Banner, C.D.B., Haldenwang, W.G., and Losick, R. (1981) Promoter for a developmentally regulated gene in Bacillus subtilis. Cell 25: 783-791.
39. Murakami, K., Fujita, N., and Ishihama, A. (1996) Transcription factor recognition surface on the RNA polymerase alpha subunit is involved in contact with the DNA enhancer element. EMBO J 15: 4358-4367.
40. Murakami, K., Kimura, M., Owens, J.T., Meares, C.F., and Ishihama, A. (1997a) The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element. Proc Natl Acad Sci USA 94: 1709-1714.
41. Murakami, K., Owens, J.T., Belyaeva, T.A., Meares, C.F., Busby, S.J., and Ishihama, A. (1997b) Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors. Proc Natl Acad Sci USA 94: 11274-11278.
42. 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.
43. Newlands, J.T., Josaitis, C.A., Ross, W., and Gourse, R.L. (1992) Both fis-dependent and factor-independent upstream activation of the rrnB P1 promoter are face of the helix dependent. Nucleic Acids Res 20: 719-726.
44. 32 in vitro. J Bacteriol 175: 661-668.
45. Perez-Martin, J., Rojo, F., and DeLorenzo, V. (1994) Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol Rev 58: 268-290.
46. Rao, L., Ross, W., Appleman, J.A., Gaal, T., Leirmo, S., Schlax, P.J., et al. (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.
47. 70), promoters, and the kinetics of the steps of transcription initiation. In Escherichia Coli and Salmonella: Cellular and Molecular Biology, 2nd edn. Neidhardt, F.C., Curtiss, R., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., et al. (eds). Washington, DC: American Society for Microbiology, pp. 792-820.
48. Rosenberg, M., and Court, D. (1979) Regulatory sequences involved in the promotion and termination of RNA transcription. Ann Rev Genet 13: 319-353.
49. Ross, W., Gosink, K.K., Salomon, J., Igarashi, K., Zou, C., Ishihama, A., et al. (1993) A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262: 1407-1413.
50. Ross, W., Aiyar, S.E., Salomon, J., and Gourse, R.L. (1998) Escherichia coli promoters with UP elements of different strength: modular structure of bacterial promoters. J Bacteriol 180: 5375-5383.
51. Russo, F.D., and Silhavy, T.J. (1992) Alpha: the Cinderella subunit of RNA polymerase. J Biol Chem 267: 14515-14518.
52. Strainic, 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. Tagami, H., and Aiba, H. (1999) An inactive open complex mediated by an UP element at Escherichia coli promoters. Proc Natl Acad Sci USA 96: 7202-7207.
54. 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.
55. Travers, A.A. (1990) Why bend DNA? Cell 60: 177-180.
56. Zhang, G., and Darst, S.A. (1998) Structure of the Escherichia coli RNA polymerase α subunit amino-terminal domain. Science 281: 262-266.
57. Zhang, G., Campbell, E.A., Minakhin, L., Richter, C., Severinov, K., and Darst, S.A. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Angstrom resolution. Cell 98: 811-824.