rRNA Promoter Regulation by Nonoptimal Binding of If Region 1.2: An Additional Recognition Element for RNA Polymerase

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2006.04.034 Byline: Shanil P. Haugen (1), Melanie B. Berkmen (1), Wilma Ross (1), Tamas Gaal (1), Christopher Ward (1), Richard L. Gourse (1) Abstract: Regulation of transcription initiation is generally attributable to activator/repressor proteins that bind to specific DNA sequences. However, regulators can also achieve specificity by binding directly to RNA polymerase (RNAP) and exploiting the kinetic variation intrinsic to different RNAP-promoter complexes. We report here a previously unknown interaction with Escherichia coli RNAP that defines an additional recognition element in bacterial promoters. The strength of this sequence-specific interaction varies at different promoters and affects the lifetime of the complex with RNAP. Selection of rRNA promoter mutants forming long-lived complexes, kinetic analyses of duplex and bubble templates, dimethylsulfate footprinting, and zero-Angstrom crosslinking demonstrated that I subunit region 1.2 directly contacts the nontemplate strand base two positions downstream of the -10 element (within the 'discriminator' region). By making a nonoptimal I1.2-discriminator interaction, rRNA promoters create the short-lived complex required for specific responses to the RNAP binding factors ppGpp and DksA, ultimately accounting for regulation of ribosome synthesis. Author Affiliation: (1) Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, Madison, WI 53706, USA Article History: Received 14 January 2006; Revised 16 March 2006; Accepted 11 April 2006 Article Note: (miscellaneous) Published: June 15, 2006