Topography of lacUV5 initiation complexes

Formation of a transcriptionally competent open complex is a highly regulat ed multistep process involving at least two intermediates. The rate of form ation and stability of the intermediate complexes often determine promoter strength. However, the detailed mechanism of formation of the open complex and the high resolution structures of these intermediates are not known. In this study the structures of the open and intermediate complexes formed on the lacUV5 promoter by Escherichia coli RNA polymerase were analyzed using 'zero length' DNA-protein cross-linking. In both the open and the intermed iate complexes the core subunits (beta' and beta) interact with lacUV5 DNA in a similar way, forming DNA-protein contacts flanking the initiation site . At the same time, the recognition (sigma (70)) subunit closely interacts with the promoter only in the open complex. In combination with our previou s results, the data suggest that during promoter recognition contacts of th e sigma subunit with core RNA polymerase and promoter DNA are rearranged in concert. These rearrangements constitute a landmark of transition from the intermediate to the open complex, identifying the sigma subunit as a key p layer directing formation of the open complex.