Key Roles of the Downstream Mobile Jaw of Escherichia coli RNA Polymerase in Transcription Initiation

Differences in kinetics of transcription initiation by RNA polymerase (RNAP) at different promoters tailor the pattern of gene expression to cellular needs. After initial binding, large conformational changes occur in promoter DNA and RNAP to form initiation-capable complexes. To understand the mechanism and regulation of transcription initiation, the nature and sequence of these conformational changes must be determined. Escherichia coli RNAP uses binding free energy to unwind and separate 13 base pairs of lambda P-R promoter DNA to form the unstable open intermediate 12, which rapidly converts to much more stable open complexes (I-3, RPo). Conversion of I-2 to RPo involves folding/assembly of several mobile RNAP domains on, downstream duplex DNA. Here, we investigate effects of a 42 residue deletion in the mobile beta' jaw (Delta JAW) and truncation of promoter DNA beyond +12 (DT+12) on the steps of initiation We find that in stable Delta JAW open complexes the downstream boundary of hydroxyl radical protection shortens by 5-10 base pairs, as compared to wild type (WT) complexes. Dissociation kinetics of open complexes formed with Delta JAW RNAP and/or DT+12 DNA resemble those deduced for the structurally uncharacterized intermediate I-3. Overall rate constants (I-3) for promoter binding and DNA opening by Delta JAW RNAP are much smaller than for WT RNAP. Values of k(a), for WT RNAP with DT+12 and full-length lambda P-R are similar, though contributions of binding and isomerization steps differ. Hence, the jaw plays major roles both early and late in RPo formation, while downstream DNA functions primarily as the assembly platform after DNA opening.