Transcription activation at class II CRP-dependent promoters: Identification of determinants in the C-terminal domain of the RNA polymerase α subunit

EMBO Journal

Volumn 17, Issue 12, 1998, Pages 3439-3447

  Savery, Nigel J ^a   Lloyd, Georgina S ^a   Kainz, Mark ^b   Gaal, Tamas ^b   Ross, Wilma ^b   Ebright, Richard H ^c,d   Gourse, Richard L ^b   Busby, Stephen J W ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^d RUTGERS UNIVERSITY   (United States)

Author keywords

Alpha subunit; Catabolite activator protein; Cyclic AMP receptor protein; RNA polymerase; Transcription activation

Indexed keywords

CYCLIC AMP; RECEPTOR PROTEIN; RNA POLYMERASE; TRANSCRIPTION FACTOR;

ARTICLE; CARBOXY TERMINAL SEQUENCE; ESCHERICHIA COLI; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; TRANSACTIVATION;

ALANINE; CYCLIC AMP RECEPTOR PROTEIN; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; MODELS, MOLECULAR; MUTAGENESIS; PLASMIDS; PROMOTER REGIONS (GENETICS); PROTEIN CONFORMATION; TRANS-ACTIVATION (GENETICS);

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 0032526956     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/17.12.3439     Document Type: Article

References (44)

1. 70 subunits of Escherichia coli RNA polymerase. J. Biol. Chem., 271, 32343-32348.
2. Attey, A., Belyaeva, T., Savery, N., Hoggett, J., Fujita, N., Ishihama, A. and Busby S (1994) Interactions between the cyclic AMP receptor protein and the alpha subunit of RNA polymerase at the E.coli gal P1 promoter. Nucleic Acids Res., 22, 4375-4380.
3. Bell, A Gaston, K., Williams, R., Chapman, K., Kolb, A., Buc, H., Minchin, S., Williams, J. and Busby, S. (1990) Mutations that alter the ability of the Escherichia coli cyclic AMP receptor protein to activate transcription. Nucleic Acids Res., 18, 7243-7250.
4. Belyaeva, T., Bown, J., Fujita, N., Ishihama, A. and Busby, S. (1996) Location of the C-terminal domain of the RNA polymerase alpha subunit I in different open complexes at the E.coli galactose operon regulatory region. Nucleic Acids Res., 24, 2243-2251.
5. 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.
6. Busby, S. and Ebright, R.H. (1994) Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell, 79, 743-746.
7. Busby, S. and Ebright, R.H. (1997) Transcription activation at class II CAP-dependent promoters. Mol. Microbiol., 23, 853-859.
8. Busby, S., Kotlarz, D. and Buc, H. (1983) Deletion mutagenesis of the Escherichia coli galactose operon promoter region. J. Mol. Biol., 167, 259-274.
9. Casadaban, M.J. and Cohen, S.N. (1980) Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J. Mol. Biol., 138, 179-207.
10. Cunningham, B. and Wells, J. (1989) High-resolution epitope mapping of hGH-receptor interactions by alanine scanning mutagenesis. Science, 244, 1081-1085.
11. Dove, S.L., Joung, J.K. and Hochschild, A. (1997) Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature, 386, 627-630.
12. Ebright, R.H. (1993) Transcription activation at class 1 CAP-dependent promoters. Mol. Microbiol., 8, 797-802.
13. Ebright, R.H. and Busby, S. (1995) The Escherichia coli RNA polymerase α subunit: structure and function. Curr. Opin. Genet. Dev., 5, 197-203.
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. Gaston, K., Bell, A., Kolb, A., Buc, H. and Busby, S. (1990) Stringent spacing requirements for transcription activation by CRP. Cell, 62, 733-743.
16. Ghosaini, L.R., Brown, A.M. and Sturtevant, J.M. (1988) Scanning calorimetric study of the thermal unfolding of catabolite activator protein from Escherichia coli in the absence and presence of cyclic mononucleotides. Biochemistry, 27, 5257-5261.
17. Jeon, Y.H., Negishi, T., Shirakawa, M., Yamazaki, T., Fujita, N., Ishihama, A. and Kyosoku, Y. (1995) Solution structure of the activator contact domain of the RNA polymerase α subunit. Science, 270, 1495-1497.
18. Kolb, A., Busby, S., Buc, H., Garges, S. and Adhya, S. (1993) Transcriptional regulation by cAMP and its receptor protein. Annu. Rev. Biochem., 62, 749-795.
19. 38 for overlapping promoters and ability to support CRP activation. Nucleic Acids Res., 23, 819-826.
20. Lloyd, G.S., Busby, S.J.W. and Savery, N.J. (1998) Spacing requirements for interactions between the C-terminal domain of the α subunit of Escherichia coli RNA polymerase and the cyclic AMP receptor protein. Biochem. J., 330, 413-420.
21. Lombardo, M., Bagga, D. and Miller, C.G. (1991) Mutations in rpoA affect expression of anaerubically regulated genes in Salmonella typhimurium. J. Bacteriol., 173, 7511-7518.
22. Miller, J. (1972) Experiments in Molecular Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
23. 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.
24. Murakami, K., Owens, J.T., Belyaeva, T.A., Meares, C.F., Busby, S.J.W. and Ishihama, A. (1997) 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.
25. Niu W., Zhou, Y. Dong, Q., Ebright, Y.W. and Ebright, R.H. (1994) Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP) I. Saturation and alanine-scanning mutagenesis. J. Mol. Biol., 243, 595-602.
26. 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.
27. Rao, L., Ross, W., Appleman, J.A., Gaal, T., Leirmo, S., Schlax, P.J., Record, M.T., Jr 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.
28. Rhodius, V.A. and Busby, S.J.W. (1998) Positive activation of gene expression. Curr. Opin. Microbiol., 1, 152-159.
29. Rhodius, V.A., West, D.M., Webster, C.L., Busby, S.J.W. and Savery, N.J. (1997) Transcription activation at class II CRP-dependent promoters: the role of different activating regions. Nucleic Acids Res., 25, 326-332.
30. Ross, W., Thompson, J.F., Newlands, J.T. and Gourse, R.L. (1990) E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. EMBO J., 9, 3733-3742.
31. Ross, W., Gosink, K.K., Salomon, J., Igarishi, 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.
32. Savery, N.J., Rhodius, V.A., Wing, H.J. and Busby, S.J.W. (1995) Transcription activation at Escherichia coli promoters dependent on the cyclic AMP receptor protein: effects of binding sequences for the RNA polymerase oc subunit. Biochem. J., 309, 77-83.
33. Severinov, K., Soushko, M., Goldfarb, A. and Nikiforov, V. (1993) Rifampicin region revisited - new rifampicin-resistant and streptolydigin-resistant mutants in the beta-subunit of Escherichia coli RNA-polymerase. J. Biol. Chem., 268, 14820-14825.
34. Simons, R.W., Houman, F. and Kleckner, N. (1987) Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene, 53, 85-96.
35. 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.
36. Tang, H., Severinov, K., Goldfarb, A. and Ebright, R.H. (1995) Rapid RNA polymerase genetics: one-day, no-column preparation of reconstituted recombinant Escherichia coli RNA polymerase. Proc. Natl Acad. Sci. USA, 92, 4902-4906.
37. West, D., Williams, R., Rhodius, V., Bell, A., Sharma, N., Zou, C., Fujita, N., Ishihama, A. and Busby, S. (1993) Interactions between Escherichia coli cyclic AMP receptor protein and RNA polymerase at class II promoters. Mol. Microbiol., 10, 789-797.
38. Wood, L.F., Tszine, N.Y. and Christie, G.E. (1997) Activation of P2 late transcription by P2 Ogr protein requires a discrete contact site on the C-terminus of the α subunit of Escherichia coli RNA polymerase. J. Mol. Biol., 274, 1-7.
39. Zalenskaya, K., Lee, J.Y., Gujuluva, C.N., Shin, Y.K., Slutsky, M. and Goldfarb, A. (1990) Recombinant RNA-polymerase-inducible overexpression, purification and assembly of Escherichia coli rpo gene-products. Gene, 89, 7-12.
40. Zhou, Y. Zhang, X. and Ebright, R. (1991) Random mutagenesis of gene-sized DNA molecules by use of PCR with Taq DNA polymerase. Nucleic Acids Res., 19, 6052.
41. Zhou, Y. Busby, S. and Ebright, R.H. (1993) Identification of the functional subunit of a dimeric transcription factor protein by use of oriented heterodimers. Cell, 73, 375-379.
42. Zhou, Y. Merkel, T.J. and Ebright, R.H. (1994a) Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP) II. Role at class I and class II CAP-dependent promoters. J. Mol. Biol., 243, 603-610.
43. Zhou, Y., Pendergrast, P., Bell, A., Williams, R., Busby, S. and Ebright, R. (1994b) The functional subunit of a dimeric transcription activator protein depends on promoter architecture. EMBO J., 13, 4549-4557.
44. Zou, C., Fujita, N., Igarishi, K. and Ishihama, A. (1992) Mapping the cAMP receptor protein contact site on the α subunit of Escherichia coli RNA polymerase. Mol. Microbiol., 6, 2599-2605.