Summary
Transcription factors interact at promoters to modulate the transcription of genes. This chapter describes three in vitro methods that can be used to monitor their activity: transcript assays, abortive initiation assays, and potassium permanganate footprinting. These techniques have been developed using bacterial systems, and can be used to study the kinetics of transcription initiation, and hence to unravel regulatory mechanisms.
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References
Browning, D. and Busby, S. (2004). The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2, 57–65.
Losick, R. and Chamberlin, M., eds. (1976). RNA Polymerase. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
Zubay, G. (1980). The isolation and properties of CAP, the catabolite gene activator. Methods Enzymol. 65, 856–877.
McClure, W. (1980). Rate-limiting steps in RNA chain initiation. Proc. Natl Acad. Sci. U. S. A. 77, 5634–5638.
Sasse-Dwight, S. and Gralla, J. (1989). KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo J. Biol. Chem.. 264, 8074–8081.
Chan, B., Minchin, S., and Busby, S. (1990). Unwinding of the duplex DNA during transcription initiation at the Escherichia coli galactose operon overlapping promoters. FEBS Lett. 267, 46–50.
Burgess, R. and Jendrisak, J. (1975). A procedure for the rapid, large-scale purification of Escherichia col i DNA-dependent RNA polymerase involving Polymin P precipitation and DNA-cellulose chromatography. Biochemistry 14, 4634–4638.
Hager, D., Jun Jin, D., and Burgess, R. (1990). Use of mono Q high resolution ionic exchange chromatography to obtain highly pure and active Escherichia coli RNA polymerase. Biochemistry 29, 7890–7894.
Tang, H., Severinov, K., Goldfarb, A., and Ebright, R. (1995). Rapid RNA polymerase genetics: one-day, no-column preparation of reconstituted recombinant Escherichia col i RNA polymerase. Proc. Natl Acad. Sci. U. S. A. 92, 4902–4906.
Fujita, N. and Ishihama, A. (1996). Reconstitution of RNA Polymerase. Methods Enzymol. 273, 121–130.
Kolb, A., Kotlarz, D., Kusano, S., and Ishihama, A. (1995). Selectivity of the Escherichia coli RNA polymerase Eσ38 for overlapping promoters and ability to support CRP activation. Nucleic Acids Res. 23, 819–826.
Sambrook, J., Fritsch, E., and Maniatis, T. (1989) Molecular Cloning. A Laboratory Manual, Second Edition. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
Savery, N., Lloyd, G., Kainz, M., Gaal, T., Ross, W., Ebright, R., Gourse, R., and Busby, S. (1998). Transcription activation at Class II CRP-dependent promoters: identification of determinants in the C-terminal domain of the RNA polymerase alpha subunit. EMBO J. 17, 3439–3447.
Herbert, M., Kolb, A., and Buc, H. (1986). Overlapping promoters and their control in Escherichia coli: the gal case. Proc. Natl Acad. Sci. U. S. A. 83, 2807–2811.
Hawley, D. and McClure, W. (1982). Mechanism of activation of transcription initiation from the λ PRM promoter. J. Mol. Biol. 157, 493–525.
Malan, T., Kolb, A., Buc, H., and McClure, W. (1984). Mechanism of CRP-cAMP activation of lac operon transcription initiation: activation of the P1 promoter. J. Mol. Biol. 180, 881–909.
Leirmo, S. and Gourse, R. (1991). Factor independent activation of E. coli rRNA transcription (I) Kinetic analysis of the role of the upstream activator region and supercoiling on transcription of the rrnB P1 promoter in vitro. J. Mol. Biol. 220, 555–568.
Rhodius, V., West, D., Webster, C., Busby, S., and Savery, N. (1997). Transcription activation at Class II CRP-dependent promoters: the role of different activating regions. Nucl. Acids Res. 25, 326–333.
Browning, D.F., Grainger, D.C., Beatty, C.M., Wolfe, A.J., Cole, J.A., and Busby, S.J. W. (2005). Integration of three signals at the Escherichia coli promoter: a role for Fis protein in catabolite repression. Mol. Microbiol. 57, 496–510.
Leirmo, S., Harrison, S., Cayley, D., and Burgess, R. (1987). Replacement of potassium chloride by potassium glutamate dramatically enhances protein DNA interactions.in vitro Biochemistry 26, 2095–2101.
Hsu, L. (1996). Quantitative parameters for promoter clearance. Methods Enzymol. 273, 59–71.
Chan, B. and Busby, S. (1989). Recognition of nucleotide sequences at the Escherichia coli galactose operon P1 promoter by RNA polymerase. Gene 84, 227–236.
Straney, D. and Crothers, D. (1985). Intermediates in transcription initiation from the E. coli lac UV5 promoter. Cell 43, 449–459.
Krummel, B. and Chamberlin, M. (1992). Structural analysis of ternary complexes of E. coli RNA polymerase: individual complexes halted along different transcription units have distinct and unexpected biochemical properties. J. Mol. Biol. 225, 221–237.
Grimes, E., Busby, S., and Minchin, S. (1991). Different thermal energy requirement for open complex formation by Escherichia coli RNA polymerase at two related promoters. Nucleic Acids Res. 19, 6113–6118.
Ponnambalam, S., Spassky, A., and Busby, S. (1987). Studies with the Escherichia coli galactose operon regulatory region carrying a point mutation that simultaneously inactivates the two overlapping promoters. Interactions with RNA polymerase and the cyclic AMP receptor protein. FEBS Lett. 219, 189–196.
Goodrich, J. and McClure, W. (1992). Regulation of open complex formation at the galactose operon promoters. Simultaneous interaction of RNA polymerase, gal repressor and CAP/cyclic AMP. J. Mol. Biol. 224, 15–29.
Bertrand-Burggraf, E., Lefevre, J. F., and Daune, M. (1984). A new experimental approach for studying the association between RNA polymerase and the tet promoter of pBR322. Nucleic Acids Res. 12, 1697–1706.
Qi, F., Liu, C., Heath, L., and Turnbough, C. (1996). In vitro assay for reiterative transcription during transcriptional initiation by Escherichia coli RNA polymerase. Methods Enzymol. 273, 71–85.
Menendez, M., Kolb, A., and Buc, H. (1987). A new target for CRP action at the malt promoter. EMBO J. 6, 4227–4234.
Gussin, G. (1996). Kinetic analysis of RNA polymerase-promoter interactions. Methods Enzymol. 273, 45–59.
El-Robh, M. and Busby, S. (2002). The Escherichia coli cAMP receptor protein bound at a single target can activate transcription initiation at divergent promoters: a systematic study that exploits new promoter probe plasmids. Biochem. J. 368, 835–843.
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Browning, D., Savery, N., Kolb, A., Busby, S. (2009). Assays for Transcription Factor Activity. In: Leblanc, B., Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology™, vol 543. Humana Press. https://doi.org/10.1007/978-1-60327-015-1_23
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DOI: https://doi.org/10.1007/978-1-60327-015-1_23
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