Abstract
DNA opening for transcription-competent open promoter complex (OC) formation by the bacterial RNA polymerase (RNAP) relies upon a complex network of interactions between the structurally conserved and flexible modules of the catalytic beta and beta'-subunits, RNAP-associated sigma-subunit, and the DNA. Here, we show that one such module, the beta'-jaw, functions to stabilize the OC. In OCs formed by the major sigma70-RNAP, the stabilizing role of the beta'-jaw is not restricted to any particular melted DNA segment. In contrast, in OCs formed by the major variant sigma54-RNAP, the beta'-jaw and a conserved sigma54 regulatory domain co-operate to stabilize the melted DNA segment immediately upstream of the transcription start site. Clearly, regulated communication between the mobile modules of the RNAP and the functional domain(s) of the sigma subunit is required for stable DNA opening.
Highlights
The DNA-dependent RNA polymerase (RNAP)[3] is central to all steps of transcription, the most regulated stage of gene expression
RNAP holoenzyme containing 54 relies on specialized activator proteins that belong to the AAA (ATPases associated with various cellular activities) family to convert the closed complex to the open complex
The results of this study provide insights into how DNA opening and open complex formation by the two mechanistically distinct types of the bacterial RNAP might occur; and provides one example of how regulated communication between the mobile modules of the RNAP and a functional domain of the subunit is required to establish the transcription proficient open complex
Summary
The DNA-dependent RNA polymerase (RNAP)[3] is central to all steps of transcription, the most regulated stage of gene expression. The molar ratio of E54 to DNA was adjusted so that approximately equal amounts of E54 closed complexes were formed in reactions containing either the mutant or wild-type RNAP (Fig. 2C, lanes 2 and 3).
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