RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription

Abstract

ABSTRACTAll organisms--bacteria, archaea, and eukaryotes--have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription-initiation-factor structural module pre-organizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription-initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate, and define details of, stepwise, RNA-extension-driven displacement of the “σ finger” of the bacterial transcription initiation factor σ. The structures reveal that--for both the primary σ factor and extracytoplasmic (ECF) σ factors, and for both 5’-triphosphate RNA and 5’-hydroxy RNA--the “σ finger” is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5’-end, upon extension of nascent RNA from ∼5 nt to ∼10 nt.SIGNIFICANCE STATEMENTThe “σ finger” of the bacterial initiation factor σ binds within the RNA polymerase active-center cleft and blocks the path of nascent RNA. It has been hypothesized that the σ finger must be displaced during initial transcription. By determining crystal structures defining successive steps in initial transcription, we demonstrate that the σ finger is displaced in stepwise fashion, driven by collision with the RNA 5’-end, as nascent RNA is extended from ∼5 nt to ∼10 nt during initial transcription, and we show that this is true for both the primary σ factor and alternate σ factors. Stepwise displacement of the σ finger can be conceptualized as stepwise compression of a “protein spring” that stores energy for subsequent breakage of protein-DNA and protein-protein interactions in promoter escape.