Transcription is the process of making an RNA copy of one of the strands of DNA. It initiates at DNA regions called promoters. In bacteria, as in other organisms, regulation of gene expression is carried out primarily by controlling the extent of transcription resulting in the mRNA which programs the amino acid sequence during protein synthesis. We are interested in the role of the bacterial "sigma" class of transcription initiation factors. These proteins impart on RNA polymerase the ability both to recognize promoter DNA, and to orchestrate the strand separation that accompanies formation of a transcription-competent RNA polymerase-promoter complex.
Koo, B.-M., Rhodius, V.A., Nonaka, deHaseth, P.L. and Gross, C.A. 2009. Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition. Genes & Dev. 23, 2426-2436. PMCID: PMC2764494
deHaseth, P.L., Gott, J.M. 2010. Conformational flexibility of s70 in anti-terminator loading. Mol. Microbiol. 75, 543-546. (commentary).
Saecker, R.M., Record, Jr., M.T. and deHaseth, P.L. 2011. Mechanism of bacterial transcription initiation: RNA polymerase-promoter binding, isomerization to initiation-competent complex, and initiation of RNA synthesis. J. Mol. Biol. 412, 754-771.
Tomsic, M., Tsujikawa, L., Panaghie. G., Wang, Y., Azok, J. and deHaseth, P.L. 2001. Different roles for basic and aromatic amino acids in conserved region 2 of E. coli ?70 in the nucleation and maintenance of the single stranded DNA bubble in open RNA polymerase-promoter complexes. J. Biol. Chem. 276, 31891-31896.
Auble, D.T. and deHaseth, P.L. 2002. Transcription. Contribution to “Encyclopedia of Genetics”, R. Robinson, editor. Macmillan Reference USA, New York.
Tsujikawa,L., Tsodikov, O.V. and deHaseth, P.L. 2002. Interaction of RNA polymerase with forked DNA: evidence for two kinetically significant intermediates on the pathway to the final complex. Proc. Natl. Acad. Sci. USA 99, 3493-3498.
Tsujikawa, L., Strainic, M.G., Wathrob, H., Barkley, M.D. and deHaseth, P.L. 2002. RNA polymerase alters the mobility of an A-residue crucial to polymerase-induced melting of promoter DNA. Biochemistry 41, 15334-15341.
Wang, Y. and deHaseth, P.L. 2003. Sigma 32-dependent promoter activity in vivo. Sequence determinants of the GroE promoter. J. Bact. 185, 5800-5806.
deHaseth, P.L. and Tsujikawa, L. 2003. Probing the role of region 2.3 of E. coli sigma 70 in the nucleation and maintenance of the single stranded DNA bubble in RNA polymerase-promoter open complexes. Methods in Enzymology 370, 553-567.
deHaseth, P.L. and Nilsen, T.W. 2004. When a part is as good as the whole. Science 303, 1307-1308. (commentary)
Sun, L., Dove, S.L., Panaghie, G., deHaseth, P.L., and Hochschild, A. 2004. An RNA polymerase mutant deficient in DNA melting facilitates study of activation mechanism: Application to an artificial activator of transcription. J. Mol. Biol. 343, 1171-1182 (2004).
Schroeder, L.A. and deHaseth, P.L. 2005. Mechanistic differences in promoter DNA melting by Thermus aquaticus and Escherichia coli RNA polymerases. J. Biol. Chem 280, 17422-17429.
Kourennaia, O.V., Tsujikawa, L. and deHaseth, P.L. 2005. Mutational analysis of Escherichia coli heat shock transcription factor sigma 32 reveals similarities with sigma 70 in recognition of the -35 promoter element and differences in promoter DNA melting and -10 recognition. J. Bact. 187, 6762-6769.
Schroeder, L.A., Choi, A.-J. and deHaseth, P.L. 2007. The –11A of promoter DNA and two conserved amino acids in the melting region of ?70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact. Nucleic Acids Research 35, 4141-4153.
Cook, V.M. and deHaseth, P.L. 2007. Strand opening-deficient E. coli RNA polymerase facilitates investigation of closed complexes with promoter DNA: effects of DNA sequence and temperature. J. Biol. Chem 282, 21319-21326.
Kourennaia, O.V. and deHaseth, P.L. 2007. Substitution of a highly conserved histidine in the Escherichia coli heat shock transcription factor, ?32, affects promoter utilization in vitro and leads to overexpression of the biofilm-associated Flu protein in vivo. J. Bact. 189, 8430-8436.
Schroeder, L.A. and deHaseth, P.L. 2008. Threonine 429 of E. coli ?70 is a key participant in promoter DNA melting by RNA polymerase. J. Mol. Biol. 376, 153-165.
Schroeder, L.A., Gries T.J., Saecker, R.M., Record, Jr., M.T., Harris, M.E. and deHaseth, P.L. 2009. Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA. J. Mol. Biol. 385, 339-349.