Structural origins of <i>Escherichia coli</i> RNA polymerase open promoter complex stability
Ruth M. Saecker, James Chen, Courtney Chiu, Brandon Malone, J Sotiris, Mark Ebrahim, Laura Y. Yen, Edward T. Eng, Seth A. Darst
Abstract
, likely representing productive and unproductive forms of RPo observed in solution studies. We find that changes in the sequence and length of DNA in the transcription bubble just upstream of the start site (+1) globally alter the network of DNA-RNAP interactions, base stacking, and strand order in the single-stranded DNA of the transcription bubble; these differences propagate beyond the bubble to upstream and downstream DNA. After expanding the transcription bubble by one base (T7A1), the nontemplate strand "scrunches" inside the active site cleft; the template strand bulges outside the cleft at the upstream edge of the bubble. The structures illustrate how limited sequence changes trigger global alterations in the transcription bubble that modulate the RPo lifetime and affect the subsequent steps of the transcription cycle.