Escherichia coli RNA polymerase

Colland, F., Fujita, N., Ishihama, A., and Kolb, A. (2002) The interaction between sigmaS, the stationary phase sigma factor, and the core enzyme of Escherichia coli RNA polymerase. Genes Cells 7, 233-247. 

Greiner, D.P., Hughes, K.A., Gunasekera, A.H., and Meares, C.F. (1996) Binding of the sigma-70 protein to the core subunits of Escherichia coli RNA polymerase, studied by iron-EDTA protein footprinting. Proc. Natl. Acad. Sci. USA 93, 71-75. 

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 tr70-a cross-link to the C-terminal region of a. Biochemistry 33, 12092-12099. 

Miyake, R., Murakami, K., Owens, J.T., Greiner, D.P., Ozoline, O.N., Ishihama, A., and Meares, C.F. (1998) Dimeric association of Escherichia coli RNA polymerase alpha subunits, studied by cleavage of single-cysteine alpha subunits conjugated to iron-(S)-l-[p-(bromoacetamido)benzyl]ethylenediaminetet raacetate. Biochemistry 37(5), 1344-1349. 

Traviglia, S.L., Datwyler, S.A., and Meares, C.F. (1999) Mapping protein-protein interactions with a library of tethered cutting reagents The binding site of sigma (70) on Escherichia coli RNA polymerase. Biochemistry 38, 4259-4265. 

Harada Y, Ohara O, Takatsuki A, Itoh H, Shimamoto N, Kinosita K (2001) Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase. Nature 409 113-115... 

Williamson, P. and Felsenfeld, G. (1978) Transcription of histone-covered T7 DNA by Escherichia coli RNA polymerase. Biochemistry 17, 5695-5705. 

Results from testing against a variety of polymerase enzymes show that efavirenz is inactive up to 300 p,M for a 50% inhibition (Young et al., 1995). The polymerase enzymes studied were Moloney murine leukemia virus RT, human DNA polymerases a, 3, and 7, Escherichia coli RNA polymerase, and the Klenow fragment. Cytotoxicity studies in their primary cells and in a T-cell line reveal that efavirenz has a selectivity index of 80,000. 

N. R. Forde, D. Izhaky, G. R. Woodcock, G. J. L. Wuite and C. Bustamante, Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase. Proc. Natl. Acad, Set USA 99, 11682-11687 (2002). 

Hager, D. A. and Burgess, R. R. (1980) Elution of proteins from sodium dodecyl sulfate-polyacrylamide gels, removal of sodium dodecyl sulfate, and renaturation of enzymatic activity results with sigma subunit of Escherichia coli RNA polymerase, wheat germ DNA topoisomerase, and other enzymes. Anal Biochem 109, 76-86. 

Alternative Sigma Factors Trigger Initiation of Transcription at Different Promoters Elongation of the Transcript Termination of Transcription Comparison of Escherichia coli RNA Polymerase with DNA Poll and PolIII... 

Comparison of Escherichia coli RNA Polymerase with DNA Poll and PolIII... 

Xu M, Zhou YN, Goldstein BP et al (2005) Cross-resistance of Escherichia coli RNA polymerases conferring rifampin resistance to different antibiotics. J Bacteriol 187 2783-2792... 

MT Record Jr, WS Reznikoff, ML Craig, KL McQuade, PJ Schlax. Escherichia coli RNA polymerase (Eo70), promoters, and the kinetics of the steps of transcription initiation. In FC Neidhardt, ed. Escherichia coli and Salmonella. Cellular and Molecular Biology. Washington, DC ASM Press, 1996, pp 792-821. 

The tasks of transcriptional and translational signal recognition involve the prediction of promoters and sites that function in the initiation and termination of transcription and translation. Bacterial promoter sites, specifically the Escherichia coli RNA polymerase promoter site, are now very well characterized. The main problem is that the two conserved regions of the bacterial promoter, the -10 and -35 regions, are separated from each other by 15 to 21 bases, making the detection of the entire promoter as a single pattern difficult. Eukaryotic promoters are less well characterized than their bacterial equivalents. The major elements are the CCAAT box, GC box, TATA box and cap site. 

Viswanathan, A. and Doetsch, P.W. (1998) Effects of nonbulky DNA base damages on Escherichia coli RNA polymerase-mediated elongation and promoter clearance. J. Biol. Chem., 2Ti, 21276-21281. 

Mukherjee, K. and Chatterji, D. (1997) Studies on the omega subunit of Escherichia coli RNA polymerase-its role in the recovery of denatured enzyme activity. Eur. J. Biochem., 247, 884-889. 

Komissarova, N., and Kashlev, M. (1997b). Transcription arrest Escherichia coli RNA polymerase translocates backward, leaving the 3 end of the RNA intact and extruded. Proc. Natl. Acad. Sci. USA 94, 1755—1760. 

Korzheva, N., Mustaev, A., Nudler, E., Nikiforov, V., and Goldfarb, A. (1998). Mechanistic model of the elongation complex of Escherichia coli RNA polymerase. Cold Spring Harb. Symp. Quant. Biol. 63, 337-345. 

Zhang, G., and Darst, S. A. (1998). Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. Science 281(5374), 262-266. 

Thomson, N. H., Smith, B. L., Almqvist, N., Schmitt, L., Kashlev, M., Kool, E. T., and Hansma, P. K. 1999. Oriented, active Escherichia coli RNA polymerase An atomic force microscope study, Biophys J76,1024-1033. 

Gruber, T.M. and Gross, C.A. (2003) Assay of Escherichia coli RNA polymerase sigma-core interactions. Methods EnzymoL, 370, 206-212. 

Escherichia coli RNA-polymerase hole- and core enzymes were 95% pure by sodium dodecyl sulfate (SDS) gel electrophoresis. Enzyme activity was measured as the amount of [ C]AMP or [ C]UMP incorporated into acid-insoluble material after a 10-min incubation at 37°. The assay mixture contained in 0.1 ml 40 mM Tris-chloride at pH 8.0, 8 mM MgCl2, 5 mAf dithioerythritol, 0.2 Azoo unit of poly[d(AT)], 0.05 M KCl, 1 mAf ATP, and 1 mAf [ C]UTP. For kinetic studies, a fixed concentration of ATP (0.4 mAf) was used and the concentration of [ C]UTP was varied. Enzyme activity was measured as the amount of [ C]UTP incorporated into acid-insoluble material after 5 min. 

Sanchez A, Garcia HG, Jones D, Phillips R, Kondev J (2011) Effect of promoter architecture on the cell-to-cell variability in gene expression. PLOS Comput Biol 7 el001100 Schulz A, Langowski J, Rippe K (2000) The effect of the DNA conformation on the rate of NtrC activated transcription of Escherichia coli RNA polymerase sigma(54) holoenzy me. J Mol Biol 300 709-725... 

Gentz, R., and Bujard, H. (1985) Promoters recognized by Escherichia coli RNA polymerase selected by function highly efficient promoters from bacteriophage T5, JBacteriol 164, 70-77. 

Kubori, T., Shimamoto, N. Physical interference between Escherichia coli RNA polymerase molecules transcribing in tandem enhances abortive synthesis and mis-incorporation. N.A.R. 25, 2640-2647 (1997)... 

Dubendorff, J W, deHaseth, P L., Rosendahl, M. S., and Caruthers, M. H. (1987) DNA functional groups required for the formation of open complexes between Escherichia coli RNA polymerase and the X P promoter. J Biol Chem 262, 892-898. 

Brautigam, a. R., Sauerbier W. Transcription unit mapping in bacteriophage T7. I. In vivo transcription by Escherichia coli RNA polymerase. J. Virol., 12, 882-886... 

Chamberlin, M., Ring, J. Studies of the binding of Escherichia coli RNA polymerase to DNA. V. T7 RNA chain initiation by enzyme-DNA complexes. J. molec. Biol. 70, 221-237 (1972). 

Maitra, U., Lockwood, A. H., Dubnoff, J. S., Guha, A. Termination, release, and reinitiation of RNA chains from DNA templates by Escherichia coli RNA polymerase. Cold Spr. Harb. Symp. quant. Biol. 35, 143-156 (1970). 

Johnson, R. S. Bowers, M. Eaton, Q. Preparation and characterization of N-(l-pyrenyl) iodoacetamide-labeled Escherichia coli RNA polymerase. Biochemistry 1991,30,189-198. 

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