Structural Basis of RNA Polymerase I Transcription Initiation

Abstract

Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8 A ˚ resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from À27 to À16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.

Structural insights into transcription initiation by yeast RNA polymerase I

“…The overall architecture of this complex is very similar to our Pol I pre‐initiation complex and the Pol I initial transcribing complex reported by Engel et al (2017), despite the fact that this complex does not contain the bridging factor Rrn3.…”

“…Polymerase‐interacting regions (PIR) as introduced by Engel et al (2017) are indicated illustrating the similarity between both models.…”

“…Comparison of the overall architecture of ITC (blue, Engel et al , 2017; PDB ID 5n61) and our model of the Pol I PIC (yellow). Polymerase‐interacting regions (PIR) as introduced by Engel et al (2017) are indicated illustrating the similarity between both models.…”

“…After our work was submitted, a study describing the crystal structure of CF and cryo‐EM structures of Pol I in complex with CF and Rrn3 and of a Pol I ITC with Pol I, CF, and Rrn3 bound to a DNA–RNA transcription scaffold was published (Engel et al , 2017). The overall architectures of our model and the Pol I ITC are very similar (Fig EV5D and E).…”

RNA polymerase I activation and hibernation: unique mechanisms for unique genes

“…Promoter-attached initiation factors foster binding of RNA polymerase I (Pol I) in complex with the Rrn3 protein [11–13]. The complete assembly of enzyme and factors on the promoter constitutes the pre-initiation complex (PIC) that has been proposed to evolve from a closed to an open complex upon DNA melting, which in Pol I is independent from ATP hydrolysis [14–16]. As proposed by these authors, an initially transcribing complex (ITC) forms upon addition of the first RNA nucleotides in the presence of initiation factors, and subsequent enzyme dissociation from the PIC leads to the formation of an elongation complex (EC).…”