Transcription activation at class II CAP-dependent promoters: Two interactions between CAP and RNA polymerase

Cell

Volumn 87, Issue 6, 1996, Pages 1123-1134

  Niu, Wei ^a   Kim, Younggyu ^a   Tau, Gregory ^a   Heyduk, Tomasz ^b   Ebright, Richard H ^a  

^a RUTGERS UNIVERSITY   (United States)

^b SAINT LOUIS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA; CYCLIC AMP; CYCLIC AMP BINDING PROTEIN; DNA; RNA POLYMERASE;

AMINO ACID SUBSTITUTION; ANISOTROPY; ARTICLE; CONTROLLED STUDY; DNA BINDING; DNA PROTEIN COMPLEX; ELECTROPHORETIC MOBILITY; GENE MUTATION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; SURFACE CHARGE; TRANSCRIPTION INITIATION;

EID: 0030582675     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)81806-1     Document Type: Article

References (42)

1. Atlung, T., Nielsen, A., Rasmussen, L.J., Nellemann, L., and Holm, F. (1991). A versatile method for integration of genes and gene fusions into the lambda attachment site of Escherichia coli. Gene 107, 11-17.
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 Escherichia coli galactose p1 promoter. Nucl. Acids Res. 22, 4375-4380.
3. Barberis, A., Pearlborg, 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.
4. 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. Nucl. Acids Res. 18, 7243-7250.
5. Belyaeva, T., Bown, J., Fujita, N., Ishihama, A., and Busby, S. (1996). Location of the C-terminal domain of the RNA polymerase alpha subunit in different complexes at the Escherichia coli galactose operon regulatory region. Nucl. Acids Res. 24, 2243-2251.
6. Blatter, E., Ross, W., Tang, H., Gourse, R., and Ebright, R. (1994). Domain organization of RNA polymerase alpha subunit. Cell 78, 889-896.
7. Borukhov, S., and Goldfarb, A. (1993). Recombinant Escherichia coli RNA polymerase. Protein Express. Purif. 4, 503-511.
8. Burgess, R., and Jendrisak, J. (1975). A procedure for the rapid, large-scale purification of Escherichia coli DNA-dependent RNA polymerase involving Polymin P precipitation and DNA-cellulose chromatography. Biochem. J. 14, 4634-4638.
9. Busby, S., and Ebright, R. (1994). Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79, 743-746.
10. Chen, Y., Ebright, Y., and Ebright, R. (1994). Identification of the target of a transcription activator protein by protein-protein photocrosslinking. Science 265, 90-92.
11. Cunningham, B., and Wells, J. (1989). High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science 244, 1081-1085.
12. Ebright, R. (1993). Transcription activation at Class I CAP-dependent promoters. Mol. Microbiol. 8, 797-802.
13. Ebright, Y., Chen, Y., Kim, Y., and Ebright, R. (1996). S-[2-(4-azidosalicylamido)ethanethio]-2-thiopyridine: radioiodinatable, cleavable photoactivatible crosslinking agent. Bioconjug. Chem. 7, 380-384.
14. Eschenlauer, A., and Reznikoff, W. (1991 ). Escherichia coli catabolite gene activator protein mutants defective in positive control of lac operon transcription. J. Bacteriol. 173, 5024-5029.
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. Hasan, N., Koob, M., and Szybalski, W. (1994). Escherichia coli genome targeting, I.Cre-lox-mediated in vitro generation of ori plasmids and their in vivo chromosomal integration and retrieval. Gene 150, 51-56.
17. Heyduk, T., Lee, J., Ebright, Y., Blatter, E., Zhou, Y., and Ebright, R. (1993). CAP-RNA polymerase interaction in solution in the absence of promoter DNA. Nature 364, 548-549.
18. Igarashi, K., and Ishihama, A. (1991). Bipartite functional map of the E. coli RNA polymerase alpha subunit. Cell 65, 1015-1022.
19. Igarashi, K., Hanamura, A., Makino, K., Aiba, H., Mizuno, T., Nakata, A., and Ishihama, A. (1991). Functional map of the alpha subunit of Escherichia coli RNA polymerase: two modes of transcription activation by positive factors. Proc. Natl. Acad. Sci. USA 88, 8958-8962.
20. Irwin, N., and Ptashne, M. (1987). Mutants of the catabolite activator protein of Escherichia coli that are specifically defective in the gene-activation function. Proc. Natl. Acad. Sci. USA 84, 8315-8319.
21. 70 subunit of Escherichia coli RNA polymerase. J. Biol. Chem. 270, 19213-19216.
22. Kolb, A., Busby, S., Buc, H., Garges, S., and Adhya, S. (1993a). Transcriptional regulation by cAMP and its receptor protein. Ann. Rev. Biochem. 62, 749-795.
23. Kolb, A., Igarashi, K., Ishihama, A., Lavigne, M., Buckle, M., and Buc, H. (1993b). E. coli RNA polymerase, deleted in the C-terminal part of its alpha-subunit, interacts differently with the cAMP-CRP complex at the lacP1 and at the galP1 promoter. Nucl. Acids Res. 21, 319-326.
24. Kunkel, T., Bebenek, K., and McClary, J. (1991). Efficient site-directed mutagenesis using uracil-containing DNA. Meth. Enzymol. 204, 125-138.
25. McClure, W. (1980). Rate-limiting steps in RNA chain initiation. Proc. Natl. Acad. Sci. USA 77, 5634-5638.
26. Niu, W., Zhou, Y., Dong, Q., Ebright, Y., and Ebright, R. (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.
27. Parkinson, G., Wilson, C., Gunasekera, A., Ebright, Y., Ebright, R., and Berman, H. (1996). Structure of the CAP-DNA complex at 2.5 Å resolution. J. Mol. Biol. 260, 395-408.
28. Sabourin, D., and Beckwith, J. (1975). Deletion of the Escherichia coli crp gene. J. Bacteriol. 122, 338-340.
29. Schickor, P., Metzger, W., Werel, W., Lederer, H., and Heumann, H. (1990). Topography of intermediates in transcription initiation of E. coli. EMBO J. 9, 2215-2220.
30. Schultz, S., Shields, G., and Steitz, T. (1991). Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253, 1001-1007.
31. Tang, H., Severinov, K., Goldfarb, A., Fenyo, D., Chait, B., and Ebright, R. (1994). Location, structure, and function of the target of a transcription activator protein. Genes Dev. 8, 3058-3067.
32. Tang, H., Severinov, K., Goldfarb, A., and Ebright, R. (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.
33. Tang, H., Kim, Y., Severinov, K., Goldfarb, A., and Ebright, R. (1996). Escherichia coli RNA polymerase holoenzyme. Meth. Enzymol., in press.
34. Tjian, R., and Maniatis, T. (1994). Transcriptional activation: a complex puzzle with few easy pieces. Cell 77, 5-8.
35. West, D., Williams, R., Rhodius, V., Bell, A., Sharma, N., Zou, C., Fujita, N., Ishihama, A., and Busby, S. (1993). Interactions between the Escherichia coli cyclic AMP receptor protein and RNA polymerase at Class II promoters. Mol. Microbiol. 10, 789-797.
36. Williams, R., Bell, A., Sims, G., and Busby, S. (1991). The role of two surface exposed loops in transcription activation by the Escherichia coli CRP and FNR proteins. Nucl. Acids Res. 19, 6705-6712.
37. Williams, R., Rhodius, V., Bell, A., Kolb, A., and Busby, S. (1996). Orientation of functional activating regions in the Escherichia coli CRP protein during transcription activation at class II promoters. Nucl. Acids Res. 24, 1112-1118.
38. Zhou, Y., Zhang, X., and Ebright, R. (1991). Random mutagenesis of gene-sized DNA molecules by use of PCR with Taq DNA polymerase. Nucl. Acids Res. 19, 6052.
39. Zhou, Y., Zhang, X., and Ebright, R. (1993a). Identification of the activating region of CAP: isolation and characterization of mutants of CAP specifically defective in transcription activation. Proc. Natl. Acad. Sci. USA 90, 6081-6085.
40. Zhou, Y., Busby, S., and Ebright, R. (1993b). Identification of the functional subunit of a dimeric transcription activator protein by use of "oriented heterodimers." Cell 73, 375-379.
41. Zhou, Y., Merkel, T., and Ebright, R. (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.
42. Zhou, Y., Pendergrast, P.S., 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.